Blog - Isos Technology

Migrating Legacy Systems to the Atlassian Cloud Ecosystem: A Comprehensive Guide

Written by Isos Technology | Apr 11, 2025

Key Takeaways

  • Legacy modernization through Atlassian Cloud migration delivers significant benefits including improved efficiency, enhanced agility, reduced costs, and better security.
  • Choose from three primary migration approaches—Fresh Start, Lift-and-Shift, or Phased Migration—based on your organization's specific needs and constraints.
  • Thorough assessment and planning are critical to successful migration, including evaluating your current environment, selecting the right cloud plan, and establishing governance frameworks.
  • Address common challenges proactively through careful data migration planning, comprehensive integration testing, and effective change management strategies.
  • Implement continuous improvement processes after migration to maximize the value of your Atlassian Cloud environment and keep pace with evolving business needs.

What is Legacy Modernization? Expert Strategies for Transforming Legacy Applications

Legacy modernization is the strategic process of updating outdated software applications and systems to align with current industry standards and evolving business needs. While legacy systems often remain functional, their outdated architecture, reliance on obsolete technologies, and integration challenges with modern solutions significantly hinder operational efficiency and innovation. By migrating these systems to modern platforms like the Atlassian Cloud ecosystem, organizations can transform aging infrastructure into valuable assets that drive business growth.

The legacy modernization journey involves much more than simply swapping old technology for new. It requires careful planning, technical expertise, and a deep understanding of business objectives. Whether you're considering a complete system replacement or targeted improvements to existing infrastructure, this guide will provide actionable insights into modernizing your legacy systems through Atlassian Cloud migration.

Why Legacy Modernization Matters in Today's Business Environment

The Hidden Costs of Maintaining Legacy Systems

Legacy systems create substantial financial and operational burdens that many organizations underestimate. Maintaining outdated technology often requires specialized skills that are increasingly rare in today's job market. As witnessed during the COVID-19 pandemic, government agencies relying on COBOL-based systems struggled to process unemployment claims due to a shortage of qualified programmers. According to industry research, organizations can spend up to 80% of their IT budgets maintaining legacy systems rather than investing in innovation.

The financial impact extends beyond direct maintenance costs. Legacy systems typically run on outdated hardware that requires frequent repairs and replacement parts that become more expensive as they grow scarcer. Security vulnerabilities in unsupported systems can lead to costly data breaches and compliance violations. By 2019, approximately one in three businesses still ran on Windows XP, exposing them to significant security risks as Microsoft ended extended support in 2014.

The Competitive Advantage of Modern Systems

Organizations that modernize their legacy applications gain significant competitive advantages through improved agility, efficiency, and innovation capabilities. Modern cloud-based systems like the Atlassian ecosystem offer scalability that legacy systems simply cannot match, allowing businesses to adapt quickly to changing market conditions and customer needs.

According to a Forrester report, organizations can achieve a 155% return on investment (ROI) within three years after migrating to cloud platforms, with a payback period of just six months. This impressive ROI stems from reduced hardware costs, decreased maintenance expenses, and operational efficiencies gained through modern application capabilities.

Types of Legacy Systems and Modernization Approaches

Common Legacy System Categories

Mainframe Systems

Financial institutions, government agencies, and organizations with high processing demands frequently rely on large-scale, centralized mainframe systems. These robust platforms have often served organizations for decades but present significant modernization challenges due to their complex architecture and specialized programming languages like COBOL.

Client-Server Applications

This architecture distributes processing between client devices (desktops, laptops) and servers. While once revolutionary, many client-server applications now struggle with modern requirements for mobility, scalability, and integration with cloud services. Modernizing these applications typically involves migrating to web-based or cloud-native architectures for improved accessibility and performance.

Monolithic Applications

Characterized by tightly coupled architecture, monolithic applications become increasingly difficult to modify and scale as business needs evolve. Modern approaches often involve decomposing these applications into smaller, independent modules or microservices for increased agility and maintainability.

Custom-Built Applications

Developed in-house to address specific business requirements, custom applications often present unique modernization challenges due to their bespoke nature. These systems may contain critical business logic that must be carefully preserved during modernization efforts.

Strategic Approaches to Legacy Modernization

Before selecting a modernization strategy, organizations must evaluate their software system's key components, including hardware infrastructure, runtime environment, development frameworks, and business logic. The optimal approach depends on the legacy system type, desired outcomes, available budget, and risk tolerance. Often, a combination of strategies provides the best solution.

Encapsulation

This relatively low-risk approach involves creating interfaces or APIs around legacy systems, allowing them to interact with modern applications without significant changes to the underlying code or infrastructure. Encapsulation provides quick integration wins while preserving existing investments.

Rehosting ("Lift and Shift")

Also known as "lift and shift," rehosting involves migrating legacy applications to newer platforms like the cloud with minimal code changes. This approach offers immediate benefits such as improved infrastructure and scalability while maintaining familiar functionality.

Replatforming

Similar to rehosting but with moderate code adjustments, replatforming helps organizations leverage new platform capabilities. This approach works well for systems that aren't overly complex and provides a balance between preservation and modernization.

Refactoring

Refactoring restructures existing code without changing external behavior, improving maintainability, testability, and performance. While more invasive than encapsulation, refactoring presents less risk than complete rewrites while delivering significant improvements.

Rearchitecting

This more radical approach involves redesigning system architecture to leverage modern technologies and design patterns. Rearchitecting can dramatically improve performance, scalability, and agility but requires substantial investment and expertise.

Rebuilding/Replacing

The most comprehensive option involves completely rebuilding or replacing legacy systems with new solutions. While expensive and time-consuming, this approach offers the greatest flexibility and innovation potential when legacy systems have become unsustainable.

Benefits of Migrating Legacy Systems to the Atlassian Cloud

Improved Efficiency and Productivity

Modernized systems streamline processes, automate manual tasks, and eliminate bottlenecks that plague legacy applications. The Atlassian Cloud ecosystem provides integrated tools that enhance collaboration and workflow efficiency across teams and departments. According to Atlassian, 99% of customers see measurable improvements in efficiency after migrating to their cloud platform.

The modular nature of modernized systems allows employees to focus on higher-value activities rather than managing technical debt or working around system limitations. Onboarding new employees becomes significantly faster with intuitive, cloud-based interfaces compared to legacy systems that often require specialized training.

Enhanced Agility and Innovation

Legacy systems typically create rigid operational constraints that slow business adaptation to market changes. The Atlassian Cloud ecosystem provides flexibility through continuous updates and new features without requiring manual upgrades or downtime. This constant evolution ensures organizations can quickly implement new capabilities as business needs change.

Cloud-based systems also facilitate easier integration with emerging technologies like artificial intelligence, machine learning, and advanced analytics. These integrations enable organizations to gain deeper insights from their data and develop innovative solutions to business challenges.

Reduced Costs and Improved ROI

Maintaining legacy systems creates significant financial burden through hardware obsolescence, expensive software licenses, and specialized skill requirements. The Atlassian Cloud ecosystem leverages subscription-based pricing that eliminates upfront capital expenditures and reduces total cost of ownership.

Cloud migration also eliminates expenses related to physical infrastructure, including server hardware, data center space, power, cooling, and maintenance. Organizations can redirect these resources toward strategic initiatives that drive business growth and competitive advantage.

Increased Security and Compliance

Legacy systems present growing security vulnerabilities as vendors discontinue support and stop releasing security patches. The Atlassian Cloud platform incorporates enterprise-grade security measures including data encryption, regular security assessments, and compliance with industry standards such as SOC 2 and ISO 27001.

Cloud providers invest heavily in security infrastructure and expertise that most organizations cannot match independently. This shared security model helps organizations improve their security posture while reducing the burden on internal IT teams.

Improved Customer and Employee Experience

Modernized systems deliver seamless, personalized experiences across channels by integrating various touchpoints and leveraging data-driven insights. The Atlassian Cloud ecosystem provides tools that enhance collaboration between teams, improving service delivery and customer satisfaction.

For employees, modernized applications significantly improve the daily work experience. Developers and architects working with cloud-based systems benefit from modern development tools, standardized interfaces, and well-documented APIs. This improved experience helps organizations attract and retain technical talent in competitive job markets.

Atlassian Cloud Migration Approaches

The Fresh Start Approach

The Fresh Start migration strategy involves setting up a new cloud instance and designing a modern, cloud-native architecture from scratch. This approach allows organizations to leave behind legacy data and configurations, creating a streamlined environment optimized for current business needs.

When to Choose This Approach

The Fresh Start strategy works best when:

  • Your current instance contains significant obsolete data or redundant configurations
  • You need to redefine workflows and processes for the cloud environment
  • You're setting up new teams or projects that benefit from a clean slate

Benefits and Challenges

Benefits:

  • Creates a streamlined, optimized environment without legacy constraints
  • Provides opportunity to redesign workflows for maximum efficiency
  • Reduces migration complexity by focusing on essential components
  • Enables faster implementation compared to other approaches

Challenges:

  • Risk of losing important historical data without careful assessment
  • Requires significant change management as employees adapt to new workflows
  • Demands thorough planning and setup of new configurations

The Lift-and-Shift Approach

The Lift-and-Shift strategy transfers existing Atlassian instances to the Cloud with minimal changes, migrating all data, users, and configurations in a single migration window. This approach maintains continuity with current setups while gaining cloud benefits.

When to Choose This Approach

Lift-and-Shift works best when:

  • You need to migrate quickly without extensive reconfiguration
  • Retaining all historical data and workflows is essential
  • You have large user bases (10,000+) or significant data volumes
  • Minimizing operational disruption is a top priority

Benefits and Challenges

Benefits:

  • Provides faster transition to cloud by moving all components simultaneously
  • Preserves historical data and familiar workflows for users
  • Simplifies the migration process by avoiding extensive redesign
  • Enables immediate access to cloud features and benefits

Challenges:

  • Extended downtime risk during the single migration window
  • Potential to migrate unnecessary data that clutters the new environment
  • Limited opportunity to optimize workflows or improve processes

The Phased Migration Approach

Phased Migration breaks down the migration process into smaller, manageable stages. This approach allows organizations to migrate data and users incrementally, often transitioning individual servers, business units, or teams separately.

When to Choose This Approach

Phased Migration works best when:

  • You have complex environments with multiple applications requiring separate migration
  • Minimizing downtime is critical for business continuity
  • You want to test cloud performance with smaller groups before full rollout
  • Managing many users and vast data makes a single migration window impractical

Benefits and Challenges

Benefits:

  • Reduces downtime by maintaining operational continuity during transition
  • Enables thorough testing at each phase to identify and resolve issues early
  • Provides flexibility to adapt strategy based on feedback from earlier phases
  • Facilitates gradual change management, reducing resistance

Challenges:

  • Requires complex coordination across multiple migration phases
  • May create temporary inconsistencies between systems during transition
  • Extends the overall migration timeline compared to other approaches

Planning Your Atlassian Cloud Migration

Assessing Your Current Environment

Before beginning migration, conduct a comprehensive assessment of your existing Atlassian environment. This evaluation should document all applications, data, dependencies, and infrastructure components. Identify inactive users, outdated projects, and unused applications that can be eliminated before migration.

Performance benchmarking is also essential during this phase. Measure current system performance to establish baselines for comparison after migration. This data helps validate migration success and identify areas for optimization in the new cloud environment.

Choosing the Right Cloud Plan

Atlassian offers several cloud plans to accommodate different organizational needs:

  • Standard: Suitable for small teams requiring core features and basic support
  • Premium: Ideal for growing teams needing advanced admin controls, unlimited storage, and enhanced performance SLAs
  • Enterprise: Best for large organizations requiring advanced compliance features, data residency options, and priority support

When selecting a plan, consider factors such as user count, storage requirements, security needs, and compliance requirements. Verify that all critical marketplace apps and integrations are compatible with your chosen plan to prevent workflow disruptions after migration.

Establishing Governance and Security Frameworks

Define clear policies for data governance, compliance, and user access in your cloud environment. Implement security best practices including identity and access management (IAM), data encryption, and continuous monitoring. Atlassian Cloud provides built-in security features like two-factor authentication and role-based access controls to protect sensitive information.

Securing stakeholder buy-in is crucial for successful migration. Present clear benefits of cloud migration, including enhanced security, reduced maintenance burden, and improved collaboration capabilities. Address stakeholder concerns proactively to build support for the transition process.

Executing Your Atlassian Cloud Migration

Building the Foundation

Before migrating data and users, establish the fundamental cloud infrastructure. Configure networks, storage, and security settings according to your organization's requirements. Set up continuous integration and deployment (CI/CD) pipelines to enable efficient operations in the cloud environment.

Implement monitoring tools like Atlassian's Opsgenie or third-party solutions to track system performance and user adoption. These tools provide valuable insights during and after migration, helping identify and address issues quickly.

Data Migration Strategies

Data migration requires careful planning to ensure integrity and minimize disruption. Use Atlassian's migration tools, such as the Cloud Migration Assistant, to transfer data efficiently. For complex migrations, consider third-party tools or services that specialize in Atlassian migrations.

Schedule data transfers during low-usage periods to reduce impact on users. Implement a robust validation process to verify data integrity after migration. This should include automated checks as well as manual verification of critical data elements.

User Transition and Training

Gradually transition users to the new cloud environment, starting with pilot groups to identify and address issues early. Provide comprehensive training resources including guided tours, documentation, and support channels to help users adapt to the new system.

Collect user feedback throughout the transition process to identify pain points and improvement opportunities. Use this feedback to refine training materials and address common issues before they impact broader user groups.

Post-Migration Optimization

Monitoring and Refining

After migration, continuously monitor system performance and user adoption. Use Atlassian's built-in analytics tools to track key metrics like response time, feature usage, and user satisfaction. Identify and address performance bottlenecks or usability issues promptly.

Optimize resource allocation based on actual usage patterns. Implement auto-scaling where appropriate to handle fluctuating workloads efficiently. Use cost management tools to track and analyze resource consumption, ensuring optimal return on investment.

Continuous Improvement

Migration to the Atlassian Cloud isn't the end of the modernization journey but rather the beginning of a continuous improvement process. Regularly assess system performance and user feedback to identify enhancement opportunities. Stay current with Atlassian's feature releases and updates to leverage new capabilities as they become available.

Conduct periodic audits to ensure compliance with security and regulatory requirements. Update governance policies and security controls as needed to address emerging threats and changing business needs.

Real-World Success Stories

Case Study: Financial Services Transformation

A leading financial institution migrated from on-premise Jira and Confluence to Atlassian Cloud to improve scalability and reduce infrastructure costs. The organization chose a phased migration approach, starting with non-critical departments to minimize business disruption.

By implementing Atlassian Cloud, the bank achieved a 3X increase in release frequency and 25% reduction in regression testing time. This resulted in substantial cost savings, improved application management, and increased customer satisfaction through enhanced stability and reduced downtime.

Case Study: Technology Company Migration

A global cybersecurity leader successfully refactored its monolithic product suite using a cloud-based platform. This modernization led to a 90% decrease in deployment time for critical services and 4X faster modernization process than manual efforts.

The company reported significant improvements in developer morale due to the improved codebase and streamlined processes. Team productivity increased dramatically as developers spent less time managing technical debt and more time delivering value to customers.

Best Practices for Legacy Modernization with Atlassian Cloud

Start with a Clear Vision and Strategy

Define specific goals, objectives, and success metrics for your modernization project. Create a vision statement that aligns with broader business objectives and communicates the value of modernization to stakeholders. This foundation guides decision-making throughout the migration process.

Adopt a Phased Approach

Break down the modernization project into smaller, manageable phases to reduce risk and ensure continuous progress. Prioritize high-value, low-risk components for initial migration to demonstrate success and build momentum. This incremental approach allows for learning and adjustment throughout the process.

Address Business Logic Early

For typical three-tier applications, start by modularizing business logic. Rewriting the user interface without addressing business logic results in only aesthetic improvements with limited functional benefits. Conversely, beginning with database modernization creates significant risk with limited room for iteration.

By modularizing business logic first, you can achieve the most significant value improvements quickly. Once business logic is modernized, you can proceed with database and user interface modernization simultaneously for comprehensive improvement.

Involve Key Stakeholders Throughout

Ensure all relevant stakeholders—including business users, technical teams, and executives—participate in planning and decision-making. Regular communication keeps everyone aligned and builds support for the modernization initiative. Create feedback channels to capture insights and concerns throughout the process.

Focus on Data Quality and Integration

During migration, verify data accuracy, consistency, and security. Plan for seamless integration between Atlassian Cloud and other business systems to maintain workflow continuity. Implement data validation procedures to identify and address issues before they impact operations.

Common Challenges and How to Overcome Them

Data Migration Complexities

Legacy systems often contain large volumes of data in non-standard formats, creating migration challenges. To address this:

  • Conduct thorough data audits before migration to identify quality issues
  • Implement data cleaning and transformation processes to ensure compatibility
  • Use specialized migration tools designed for Atlassian products
  • Perform test migrations with sample data to identify and resolve issues early

System Integration Issues

Legacy applications typically have custom interfaces or connectors that may not work with cloud environments. To overcome integration challenges:

  • Document all existing integrations and their requirements
  • Evaluate cloud-compatible alternatives for critical integrations
  • Implement middleware solutions where necessary to bridge compatibility gaps
  • Test integrations thoroughly before full migration

Resistance to Change

Users accustomed to legacy systems may resist transition to new platforms. Effective change management strategies include:

  • Communicating clear benefits of the new system to affected users
  • Providing comprehensive training and support resources
  • Involving users in testing and feedback to build ownership
  • Identifying and empowering change champions within departments

Extended Timeline and Cost Management

Legacy modernization projects often take longer and cost more than initially estimated. To manage these challenges:

  • Set realistic expectations with stakeholders about timeline and budget
  • Break the project into smaller phases with clear deliverables
  • Implement regular progress reviews and adjust plans as needed
  • Focus on high-value components that deliver quick wins

Future-Proofing Your Atlassian Cloud Environment

Embracing Continuous Modernization

Legacy modernization isn't a one-time project but an ongoing process. Establish mechanisms for continuous improvement, regularly assessing system performance and user feedback. This approach helps identify optimization opportunities and keeps your environment aligned with evolving business needs.

Leveraging Emerging Technologies

The Atlassian Cloud ecosystem continues to evolve with new capabilities and integrations. Stay informed about emerging technologies like artificial intelligence, machine learning, and advanced analytics that can enhance your cloud environment. Evaluate these technologies against business requirements to identify valuable implementation opportunities.

Building a Culture of Innovation

Successful modernization extends beyond technology to encompass organizational culture. Foster an environment that embraces change and continuous improvement. Encourage teams to experiment with new features and workflows that enhance productivity and collaboration.

FAQs About Legacy Modernization and Atlassian Cloud Migration

What exactly is legacy modernization in the context of Atlassian products?

Legacy modernization for Atlassian products involves updating or replacing outdated Server or Data Center deployments with modern Atlassian Cloud solutions. This process transforms aging systems into more agile, scalable, and efficient platforms that better support business objectives. Beyond simple migration, comprehensive modernization includes optimizing workflows, integrations, and user experiences to leverage cloud capabilities fully.

How do I determine which Atlassian Cloud migration approach is right for my organization?

Selecting the optimal migration approach depends on several factors including your current environment complexity, business continuity requirements, and modernization goals. The Fresh Start approach works best when you need a clean break from legacy configurations. Lift-and-Shift is ideal when preserving all historical data and minimizing change is critical. Phased Migration offers the best balance for complex environments where downtime must be minimized. Conduct a thorough assessment of your current state, business priorities, and technical constraints before choosing your approach.

What are the security implications of migrating from on-premise Atlassian systems to the cloud?

Migrating to Atlassian Cloud actually enhances security for most organizations. Atlassian Cloud meets rigorous security standards including SOC2, ISO 27001, and GDPR compliance. The platform provides enterprise-grade security features such as data encryption at rest and in transit, regular security assessments, and advanced access controls. Atlassian's dedicated security team continuously monitors and addresses emerging threats, providing protection that exceeds what most organizations can implement internally.

How can we minimize disruption to users during the migration process?

Minimizing disruption requires careful planning and communication. Start by creating a detailed migration timeline that schedules critical activities during low-usage periods. Implement a phased approach that transitions users gradually rather than all at once. Provide comprehensive training and support resources before, during, and after migration. Establish clear communication channels for users to report issues and receive assistance. Finally, conduct thorough testing at each migration stage to identify and resolve problems before they impact users.

What happens to our custom apps and integrations when we migrate to Atlassian Cloud?

Custom apps and integrations require careful evaluation before migration. First, determine if cloud-compatible versions exist for your custom apps. Many Marketplace apps offer cloud equivalents, but functionality may differ. For custom integrations, assess whether they use APIs compatible with Atlassian Cloud. You may need to refactor some integrations to work with cloud endpoints. In cases where no cloud alternative exists, consider rebuilding functionality using Atlassian's cloud development frameworks or finding alternative solutions that provide similar capabilities.

How long does a typical Atlassian Cloud migration take?

Migration timelines vary significantly based on environment complexity, data volume, and chosen migration approach. Simple migrations with limited data and few customizations might complete in weeks, while complex enterprise migrations can extend to several months or even a year. Key factors affecting timeline include the number of users, volume of historical data, complexity of workflows and customizations, and integration requirements. Creating a realistic timeline requires thorough assessment of these factors and building in contingency for unexpected challenges.

What cost savings can we expect after migrating to Atlassian Cloud?

Organizations typically realize significant cost savings after cloud migration through reduced infrastructure expenses, lower maintenance requirements, and improved operational efficiency. According to Forrester research, companies achieve an average 155% ROI within three years of migration. Direct savings come from eliminating hardware costs, reducing IT staffing requirements, and avoiding expenses related to upgrades and maintenance. Indirect savings result from improved productivity, faster innovation cycles, and reduced downtime. The subscription-based pricing model also converts capital expenditures to operational expenses, improving financial flexibility.

How do we ensure data integrity during the migration process?

Ensuring data integrity requires a systematic approach to data migration. Begin with comprehensive data mapping that identifies all data sources and their destinations in the cloud environment. Implement data validation checks at multiple stages: pre-migration to establish baselines, during migration to verify transfer accuracy, and post-migration to confirm completeness and correctness. Use Atlassian's migration tools which include built-in validation capabilities. For critical data, consider parallel operation periods where both systems run simultaneously to verify consistency before decommissioning legacy systems.

What training resources are available to help our teams adapt to Atlassian Cloud?

Atlassian provides extensive training resources to support cloud migration and adoption. These include documentation, video tutorials, webinars, and guided learning paths through Atlassian University. The Atlassian Community offers forums where users can ask questions and share experiences. For organizations requiring more structured training, Atlassian Solution Partners provide customized training programs tailored to specific team needs. Consider implementing a digital adoption platform that provides in-app guidance to help users navigate new interfaces and workflows effectively.

How can we measure the success of our legacy modernization project?

Successful modernization projects require clear, measurable objectives established before migration begins. Technical metrics should include system performance (response time, uptime, error rates), security compliance, and integration effectiveness. Business metrics might encompass user adoption rates, productivity improvements, time-to-market reductions, and cost savings. User satisfaction metrics provide insight into how well the new system meets user needs. Establish baseline measurements before migration and track changes over time to demonstrate improvement. Regular stakeholder reviews help ensure the modernization delivers expected business value.

Sources:
vFunction
Deviniti
Atlassian
Whatfix
Skytap