The top Atlassian Jira integration apps fall into two categories: template-based solutions like Zapier (best for simple workflows) and script-based platforms like Exalate (best for complex enterprise needs).
Choose template-based for quick setup with standard processes, or script-based for customizable, sophisticated integrations.
What You’ll Learn In This Guide:
This comprehensive guide helps you select the right Jira integration tool by comparing:
- 6 leading marketplace apps with detailed feature breakdowns
- Template vs. script-based solutions and when to use each
- Real-world use cases from MSPs, enterprises, and DevOps teams
- Implementation best practices to avoid common pitfalls
Why Jira Integration Matters
With hundreds of integration apps available in the Atlassian Marketplace, choosing the wrong tool can lead to wasted resources, failed implementations, and frustrated teams. The right integration eliminates manual data entry, keeps teams aligned across platforms, and scales with your business needs.
Whether you’re connecting Jira with ServiceNow, Zendesk, Salesforce, or other Jira instances, this guide provides the clarity you need to make an informed decision based on security, versatility, customizability, and your team’s technical capabilities.
What Are Jira Integration Apps Used For
Here are detailed use cases for Jira integration tools with real-world scenarios:
Cross-Team Collaboration and Task Creation
Jira integrations can help teams automate task or work item creation in real time. Picture a company where the DevOps team uses Jira Service Management for IT operations, while the other teams use Jira Cloud and Jira Software for development workflows.
Netguru connected its DevOps team’s internal Jira Service Management with other teams, allowing them to keep track of more than 100 active commercial projects.
So when developers mark a feature as “Done” in Jira Software, the integration automatically creates a task in Jira Service Management for the DevOps team to get instant updates.
Support Ticket Escalation and Routing
A B2B software company receives bug reports through Zendesk from paying customers. Their integration automatically creates tickets in Jira Software. P1 bugs from enterprise customers go directly to senior developers, while general feature requests get routed to the product backlog.
If a critical bug isn’t acknowledged within 30 minutes, it automatically escalates to the engineering manager and creates a parallel incident in their monitoring system.
When enterprise customers submit requests, they bypass the general queue and go straight to dedicated account managers, who can automatically escalate complex issues to technical specialists.
Turkey’s biggest insurance company used this integration option to maintain seamless, flexible synchronization between different Jira instances when collaborating with suppliers.
MSP (Managed Service Provider) Operations
A managed IT services company uses Jira Service Management (JSM) to handle multiple client environments. Each client gets their own service project with custom SLA rules.
When clients submit tickets through their branded portals, automated routing sends server issues to the infrastructure team, software problems to the devs, and security incidents to the SOC team.
For critical issues affecting multiple clients, the system creates master incident tickets that link to individual client tickets, allowing coordinated resolution while maintaining separate client reporting.
The Gantner Group established a frictionless collaboration ecosystem between developers and support staff, which increased resolution speed by 50 times.
ITSM Enterprise Workflow Integration
A manufacturing company uses JSM as its central ITSM platform, integrated with ServiceNow for incident tracking.
When employees submit service requests through the corporate portal, automated routing sends hardware requests to field services, software requests to the applications team, and access requests to security teams.
The integration pulls configuration data from their CMDB in ServiceNow to identify affected systems and automatically notify relevant stakeholders.
If changes fail, the system creates rollback tasks and incident tickets while updating the knowledge base with lessons learned for future reference.
Project Visibility and Stakeholder Updates
An enterprise wants to automatically create weekly update tasks for project managers when milestones are reached or deadlines approach.
For internal operations, their facilities team uses Jira Service Management with automated routing based on request type and location. Office supply requests go to local administrators, while IT equipment requests are routed to the central IT team.
The system includes escalation rules for urgent requests like broken air conditioning or security access issues, automatically notifying facility managers and creating emergency response tasks.
Multi-Instance Management with Centralized Routing
A global tech company runs multiple Jira Cloud instances with a master routing system. When issues affect multiple regions, the system creates synchronized tickets across relevant instances and establishes parent-child relationships.
For example, when a security vulnerability is discovered, the system creates tickets in each regional Jira Software instance and establishes escalation paths to security teams in each timezone.
SPK, a managed service provider, was able to create unidirectional sync between its Jira instances, eliminating the manual process of checking tickets across instances.
Their global help desk uses centralized routing logic that considers time zones, language preferences, and expertise.
What Are Key Features to Look for in Atlassian Jira Sync Apps
- Bidirectional vs. unidirectional sync capabilities: Choose between two-way sync for collaborative workflows or one-way sync for migration, merger, and acquisition scenarios.
- Field mapping flexibility: Map different field names and formats between systems. Transform data types and values automatically.
- Real-time vs. batch synchronization: Choose between immediate updates or scheduled bulk syncing based on your needs.
- Support for custom fields and complex data types: Confirm the ability to handle enterprise Jira configurations, including custom fields, attachments, and linked issues.
- Performance and scalability considerations: Look for a Jira integration in the marketplace that can handle high-volume sync operations and large data sets without degradation as your organization grows.
- Security and compliance features: Prioritize security features such as enterprise-grade authentication, encryption, and audit trails for regulatory requirements.
- Error handling and recovery: Account for graceful failure management with retry logic and clear error reporting when sync operations fail.
- AI-powered integration: Automated script generation and intelligent mapping suggestions that reduce setup time and technical complexity.
- Comprehensive activity logging and monitoring: You need detailed sync logs, performance metrics, and alerting for operational visibility.
Template-Based vs. Script-Based Atlassian Jira Integration Apps: Which One is Better?
Template-based solutions offer pre-built configurations for common integration scenarios. You get to select from existing templates or connectors and configure basic settings like field mappings and sync frequency.
Some advantages of templated Atlassian Jira integrations include:
- Fewer technical skill requirements
- Lower implementation costs and faster time-to-value
- Quick setup and deployment, often within hours
- Lower risk of configuration errors
- Less maintenance overhead
Template-based solutions have significant constraints when it comes to unique business processes. They can’t handle complex data transformations or support all field types and custom configurations. They’re also difficult to adapt when business requirements change and often create rigid workflows that don’t match specific organizational needs.
Script-based solutions like Exalate use programming languages (typically Groovy or JavaScript) to define custom sync logic. You write code to specify exactly how data should transform, filter, and flow between systems.
Some advantages of scripted Jira integrations include:
- Handle complex business logic and data transformations
- Support for advanced conditional logic and routing
- Can evolve and scale with changing business requirements
- Handle edge cases and exceptions gracefully
- Adapt to unique organizational workflows
- Unlimited customization possibilities
The major hurdle when using script-based Atlassian Jira integrations is that they might require dedicated technical resources to set up the integration and maintain it.
However, with AI, both these types of integrations can be improved significantly. Using AI-powered solutions for template-based apps would mean creating automated mappings and templates, but in essence, it will still be limited by the actual use cases the solution can provide. Adding an AI layer at the top just creates simplicity.
In contrast, AI-powered integrations provide more value to the users since they can customize any use case using natural language prompts. The scripts for the use case will be generated automatically. This makes it more valuable for the users since they get the power of customization and the ease of AI combined in a single place.
Which Atlassian Jira Integration Approach is Better?
Template-based apps work best when you have standard, straightforward sync requirements and need quick deployment with limited technical resources.
They’re ideal for common system combinations with standard field mappings where your integration needs are unlikely to change significantly. For instance, you can use them to sync work item descriptions, comments, and attachments by default.
Script-based apps become essential when your business processes are unique or complex, requiring sophisticated data transformation logic that templates can’t handle.
They’re particularly valuable when connecting multiple systems with complex relationships or when compliance and security requirements demand specific handling approaches.
This gives you the best of both worlds—rapid deployment for standard scenarios with the flexibility to customize when requirements get complex.
The Best Template-Based Atlassian Marketplace Apps for Jira Integrations
Zapier Integration for Jira
Zapier integration for Jira offers thousands of pre-built templates connecting Jira to popular business tools like Slack, Google Sheets, Trello, and email platforms. Their “Zaps” provide simple trigger-action workflows—when a Jira issue gets created, automatically post to Slack.
The templates cover common scenarios like customer support workflows, project notifications, and reporting automation. Setup takes minutes with no coding required, making it ideal for small teams needing basic integrations.
Zapier does not support customization for complex business logic because it’s designed for simple trigger-action workflows.
Getint
Getint offers template-driven integrations designed explicitly for project management workflows. Their pre-built templates connect Jira with tools like Microsoft Project, Smartsheet, and other project management platforms.
The templates focus on project portfolio management scenarios, handling resource planning, timeline synchronization, and progress reporting.
While Getint does offer some scripting capabilities through JavaScript for custom transformations, these scripts are limited to data manipulation during sync rather than full bidirectional logic control. You can transform field values and apply conditional mappings, but you can’t fundamentally alter the sync architecture or create complex multi-system orchestration like true script-based solutions allow.
Getint’s templates are powerful for organizations needing to bridge agile development in Jira with traditional project management approaches. However, this restricts its flexibility for unique business processes, forcing organizations to adapt their workflows to fit predefined mappings rather than customizing the integration to match their specific requirements. Even with scripting, the underlying template structure constrains what’s possible.
Backbone Issue Sync
Backbone provides template-based synchronization between multiple Jira instances and external systems. Their templates handle common scenarios like cross-instance project synchronization, customer portal integrations, and multi-tenant environments.
The templates are designed for organizations managing multiple Jira deployments who need standardized sync patterns across different instances. Backbone excels at handling complex organizational structures with minimal configuration effort.
However, it is primarily focused on Jira-to-Jira integration with limited support for external systems, making it unsuitable for integrating Jira with other third-party CRM or ITSM tools.
Jira Automation
Jira Automation is Atlassian’s built-in workflow automation tool that comes free with Jira Cloud, Software, and Service Management. It allows users to create automated rules that trigger actions based on specific events within Jira.
The major drawback to Jira Automation is that it can’t sync data with external systems. Besides, you can’t set up advanced custom rules for your own automation.
The Best Script-Based Atlassian Marketplace Apps for Jira Integrations
Custom REST API Integrations
Atlassian makes it possible for developers to build custom REST API integrations using JavaScript or other scripting languages.
These solutions offer maximum flexibility for developers comfortable building integrations from scratch. They’re ideal for unique integration requirements that don’t fit standard connector patterns.
But even with the freedom that custom Jira integrations provide, they still require significant technical debt and resources to set up. You also have to invest heavily in maintenance.
Exalate
Exalate stands out as the most comprehensive script-based Jira integration app in the Atlassian Marketplace. It supports bidirectional sync between Jira and systems like ServiceNow, Salesforce, Freshservice, Service Desk Plus, Freshdesk, Ivanti, Azure DevOps, Zendesk, and other Jira instances. To get the list of platforms Exalate supports, visit the integrations page.
Exalate comes with an AI-powered Groovy scripting engine that excels at handling enterprise-grade integrations with sophisticated field mapping, conditional logic, and data transformations.
This app can manage complex scenarios like multi-instance synchronization, MSP environments with different client SLA rules, and compliance workflows requiring specific audit trails.
The one drawback to Exalate is that it requires knowledge of Groovy, but you can side-step this hurdle with the help of AI Assist.
ScriptRunner Connect
ScriptRunner Connect also uses both JavaScript/Typescript and Groovy scripting for deep Jira customizations and integrations. It provides powerful automation capabilities, including custom REST endpoints, scheduled jobs, and complex workflow logic.
It excels at internal Jira customizations and can integrate with external systems through custom scripts.
ScriptRunner Connect is a good choice for organizations needing extensive Jira workflow customization alongside integration capabilities, though it requires significant JavaScript/Typescript expertise.
Regardless, ScriptRunner Connect has a steep learning curve and high technical complexity to implement and debug problematic syncs. You need advanced JavaScript/TypeScript experience, API knowledge, and environment management expertise.
| Integration Tool | Best Use Case | Key Features |
| SCRIPT-BASED INTEGRATION APPS | ||
| Exalate | Simple to advanced enterprise integrations requiring sophisticated data transformation and mapping logic, deep ticket integration, MSP to client connections using multiple systems, orchestrating ITSM workflows end-to-end, and cross-company (or intra-company) collaboration with granular control. |
|
| ScriptRunner Connect | Flexible Jira customization and automation with extensive workflow modifications, ideal for organizations needing custom REST endpoints and complex business logic |
|
| Custom REST API | Unique integration requirements that don’t fit standard connector patterns, offering maximum flexibility for developers building from scratch. Ideal for enterprises with dedicated technical resources for development, maintenance, and upgrades. |
|
| TEMPLATE-BASED APPS | ||
| Zapier Integration for Jira | Simple trigger-action workflows connecting Jira to popular business tools like Slack, Google Sheets, and email platforms with minimal setup |
|
| GetInt | Project portfolio management scenarios needing to bridge agile development in Jira with traditional project management tools like MS Project |
|
| Backbone Issue Sync | Organizations managing multiple Jira deployments and needing standardized sync patterns across different instances with minimal configuration |
|
| Jira Automation | Internal Jira workflow optimization requiring automated task assignment, status transitions, and notification triggers within the same Jira instance |
|
Best Practices When Using Atlassian Marketplace Apps for Jira Integration
- Start with a clear integration strategy. Define your integration goals before selecting tools. Identify which systems need to connect, what data should sync, and how often updates need to happen. Map out your current workflows to understand where integration adds value versus where it might create unnecessary complexity.
- Choose the right Atlassian app for Jira integration. Evaluate whether template-based or script-based solutions fit your requirements. Consider hybrid approaches that start with templates but allow customization as needs evolve.
- Plan your field mappings before you configure. Create a comprehensive mapping document that shows how fields translate between systems. Ensure your integration can adapt to new custom fields or workflow changes without breaking existing syncs.
- Start with a pilot project. Choose a specific team, project, or use case that represents your broader needs but limits initial risk. This approach allows you to learn from real-world usage, identify unexpected challenges, and refine your approach before scaling to larger implementations.
- Implement proper filtering and sync rules. Use filters to sync only relevant tickets based on project, issue type, priority, or custom field values. Implement proper routing rules that send different types of issues to appropriate teams or systems.
- Test thoroughly before going live. Test all sync scenarios, including edge cases, bulk operations, and error conditions. Verify that field mappings work correctly and data transformations produce expected results. Test user permissions and security controls to ensure proper access restrictions are maintained across integrated systems.
- Document your configuration for future team members. Create comprehensive documentation that covers your integration architecture, field mappings, sync rules, and business logic. Include troubleshooting guides, common error scenarios, and step-by-step configuration instructions.
- Ensure security and compliance requirements. Implement proper authentication mechanisms, including OAuth or SAML, where required. Maintain audit trails for all sync activities to support compliance requirements. Review and restrict permissions to ensure users only access data they’re authorized to see.
- Plan for maintenance and updates. Stay current with app updates and security patches for all integration components. Monitor for deprecation notices from connected systems and plan migration strategies when APIs or features change.
Key Takeaways
- Atlassian Jira integration apps automate workflows between development, support, and business teams to eliminate manual updates and improve cross-system visibility.
- Essential integration features include bidirectional sync, flexible field mapping, real-time updates, filtering capabilities, security controls, and customization options.
- Template-based apps offer quick deployment for standard workflows, while script-based apps provide unlimited customization for complex business requirements.
- Top template solutions include Zapier, GetInt, and Backbone for common, straightforward integration scenarios.
- Leading script-based platforms like Exalate and ScriptRunner Connect handle complex, multi-layered enterprise integrations through scripting languages like Groovy, JavaScript, etc..
- Successful implementation requires pilot projects, thorough planning, comprehensive testing, proper documentation, and ongoing monitoring for business value.
Frequently Asked Questions
What are Atlassian Marketplace Jira integration apps?
Jira integration apps that are available on the Atlassian marketplace can connect Jira with other work management systems, ITSM tools, CRM platforms, and development tools. They automate data synchronization between systems, eliminating manual data entry and keeping teams aligned across different platforms.
What’s the difference between template-based and script-based integration apps?
Template-based apps offer pre-built configurations for common integration scenarios with a setup wizard and minimal technical requirements. Script-based apps use programming languages like Groovy or JavaScript to create custom sync logic, providing unlimited flexibility but requiring technical expertise.
How do I choose between template-based and script-based solutions?
Template-based apps offer limited customization within predefined mappings. Script-based apps provide complete control over field mappings and workflow transformations. Choose template-based apps if you have standard workflows, basic field mappings, and sync requirements. If you have unique business processes, complex data transformation needs, and integration requirements that will evolve, then you need to choose script-based Jira integration apps.
What’s the difference between bidirectional and unidirectional sync?
Bidirectional sync allows data to flow both ways between systems automatically, keeping both platforms updated in real-time. Unidirectional sync only flows data in one direction, which is helpful in reporting scenarios or when you only need updates to go from one system to another, or during migrations.
Do I need technical skills to set up a Jira integration?
It depends on the app. Template-based solutions like Zapier require minimal technical skills and can be set up in minutes. Script-based solutions like Exalate or ScriptRunner Connect require programming knowledge (typically Groovy or JavaScript) for implementation and customization. But with the advent of AI, the responsibility of writing sync scripts for script-based apps has been automated. This provides a fine balance between heavy customization through scripts and the ease of use of AI, resulting in a higher value for integration users. It’s also important to use AI judiciously, since it can still make mistakes. Human oversight is mandatory.
Can I integrate multiple Jira instances?
Yes, several apps specialize in Jira-to-Jira integration, including Backbone Issue Sync and Exalate. These apps handle multi-instance scenarios common in global organizations, MSP environments, or companies with separate Jira deployments for different departments.
What fields can I sync between Jira and other systems?
Most integration apps sync standard fields like summary, description, priority, status, assignee, comments, and attachments. Advanced script-based apps support custom fields, issue links, subtasks, sprints, epics, and even third-party plugin data like Tempo timesheets or custom field values.
How do integration apps handle conflicts when the same issue is updated in both systems simultaneously?
Conflict resolution varies by app. Basic solutions use “last update wins” logic. Advanced script-based solutions let you define custom conflict resolution rules, such as prioritizing specific field changes, manual review queues, or notifying administrators for resolution.
Can I filter which tickets get synced?
Yes, most integration apps offer filtering capabilities. You can set triggers based on project, issue type, priority, labels, custom fields, or JQL queries in Jira. This prevents unnecessary data sync and reduces noise in connected systems.
Do Jira integration apps support real-time or batch-based syncs?
Most modern integration apps support real-time synchronization, updating connected systems within seconds of changes. Some also offer scheduled batch sync options for less time-sensitive scenarios or to reduce API call volume.
How secure are Atlassian marketplace apps for Jira integration?
Reputable marketplace apps implement enterprise-grade security, including OAuth authentication, encrypted data transmission (TLS/HTTPS), role-based access controls, and audit logging. Always verify security certifications like ISO 27001 or SOC 2 compliance for sensitive data integrations. You can find out more about how Exalate handles security from the Trust Center.
What’s the difference between native integrations and marketplace apps?
Native integrations are built directly by Atlassian, or provided in the form of automations (e.g, Jira automation) or the connecting platform (like ServiceNow’s IntegrationHub). Marketplace apps are third-party solutions offering more flexibility, advanced features, and support for more platforms. Native integrations work well for basic scenarios, while marketplace apps handle complex enterprise requirements.
How do I handle data transformation when field formats differ between systems?
Script-based integration apps excel at data transformation, converting between different formats like Jira’s markdown and Azure DevOps’ HTML. They provide helper functions and transformation scripts to handle data type conversions, value mapping, and format differences automatically.
Can I integrate Jira with systems not listed in the marketplace?
Yes, script-based solutions like Exalate and ScriptRunner Connect can integrate with any system that has a REST API, though you’ll need to write custom integration code. Exalate supports bidirectional sync between Jira and systems like ServiceNow, Salesforce, Freshservice, Service Desk Plus, Freshdesk, Asana, Ivanti, Azure DevOps, Zendesk, and other Jira instances.
Do integration apps support MSP scenarios?
Yes, Exalate specifically supports MSP use cases where you need to maintain separate instances for different clients with custom SLA rules, independent access controls, and the ability to manage multiple client connections from a central MSP instance.
Can I use multiple integration apps simultaneously?
Yes, you can run multiple integration apps in Jira simultaneously to connect different systems. However, be careful to avoid creating overlapping integrations that sync the same data, as this can cause conflicts and duplicate information. You can use Zapier to create a Slack notification in the engineering team channel when a new dev issue is created, while Exalate can be used to sync the necessary ticket details like summary, desc, custom fields, labels, etc.
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