JCMA Post-Migration Checklist: What to Clean Up After Migrating Jira Data Center to Cloud

Key Takeaways

Cleanup must follow a specific order: fields first, then permissions, workflows, automation, dashboards
JCMA does not migrate automation rules or webhooks -- these need manual recreation
Complete all duplicate field cleanup before adding new custom fields to Cloud

You just finished migrating your Jira Data Center instance to Cloud using the Jira Cloud Migration Assistant (JCMA). Congratulations -- but your work is not done. In fact, the most critical phase starts now: post-migration cleanup.

Every JCMA migration leaves behind a trail of duplicate fields, orphaned configurations, broken automation rules, and stale dashboards. If you skip the cleanup steps below, your team will waste time working with fragmented data and broken workflows for weeks or months.

This checklist covers every major area you need to audit after a JCMA migration. Items are organized by priority and labeled as either Quick Win (under 30 minutes) or Deep Task (1-4 hours). Tackle the quick wins first to build momentum, then move into deeper technical tasks.

If you need background on why JCMA creates duplicate fields in the first place, see our earlier post: What Is JCMA? Why Jira Cloud Migration Assistant Creates Duplicate Fields (And How to Fix Them).

Priority 1: Duplicate Field Cleanup (Do This First)

Deep Task -- 2 to 8 hours depending on instance size

Run a full scan of all custom fields to identify every "(migrated)" duplicate pair.
Classify each pair as SAFE (same type, original empty), REVIEW_REQUIRED (different types or original has data), or CONFLICT (cannot merge safely).
Merge SAFE pairs first -- copy migrated values into originals only when the original is empty. Never overwrite existing Cloud data.
For REVIEW_REQUIRED pairs, manually decide per field whether to merge, keep both, or escalate.
Delete verified migrated fields starting with those that have zero associated issues.
Re-scan to confirm all duplicates are resolved.

For the detailed step-by-step on duplicate field cleanup, see our guide to understanding and fixing JCMA duplicate fields. For the suffix removal process specifically, see how to remove the (migrated) suffix from Jira custom fields.

Tool recommendation: Migration Field Cleanup for Jira automates the scan-detect-merge workflow. It runs entirely on Atlassian Forge (no external servers), classifies each pair automatically, and shows issue counts per field so you know the impact before merging. Free to install and scan.

Priority 2: Permission and Role Verification

Quick Win -- 1 to 2 hours

Compare permission schemes between DC and Cloud. JCMA migrates most but may miss custom permissions or project-specific overrides.
Verify that all Jira groups and users from DC exist in Cloud. Check the People section under Settings to confirm.
Audit project roles (Administrators, Developers, Users) -- JCMA may not map custom roles correctly.
Test access with a sample user from each major group. Create issues, edit fields, and transition workflows to confirm permissions work.
Check service accounts and integration users -- these often get left behind or assigned wrong permissions after migration.

Priority 3: Workflow and Screen Scheme Validation

Deep Task -- 2 to 4 hours

Compare every workflow in Cloud against your DC instance. Look for workflows that are missing post-functions, conditions, or validators.
Check that workflow statuses and transitions match. JCMA sometimes creates new status variants instead of mapping to existing ones.
Verify screen schemes -- ensure each issue type shows the correct fields. Missing screens are a common post-migration pain point.
Audit field configurations. Confirm that all custom fields (including newly merged ones) appear in the correct field configuration schemes.
Test a full issue lifecycle in each project: create, transition through every status, and resolve. Catch broken transitions early.

Priority 4: Automation Rule Audit

Deep Task -- 1 to 3 hours

Export all automation rules from Cloud and compare against your DC Automation (or ScriptRunner) rules. JCMA does not migrate automation rules.
Recreate each automation rule in Jira Cloud Automation. Pay special attention to rules that reference custom fields -- update field references after merging duplicates.
Test every automation rule with a sample issue. Rules that worked in DC may fail silently in Cloud due to different field IDs or API limits.
Check webhook configurations. If you used DC webhooks, recreate them in Cloud Automation or via the Settings > Apps > Webhooks page.
Review automation run history after one week. Look for failed runs and investigate root causes (field not found, permission denied, etc.).

Priority 5: Dashboard and Reporting Checks

Quick Win -- 1 to 2 hours

Open every shared dashboard and verify all gadgets display data correctly. Gadgets referencing deleted or renamed fields will show errors.
Rebuild any Jira Reports (Pie Chart, Filter Results, etc.) that reference custom fields. Field ID changes after migration break these reports.
Update saved filters. JQL queries using old field IDs will return zero results until updated to the surviving field.
Verify third-party reporting tools (e.g., EazyBI, Structure, BigPicture). These often need reconfiguration after a migration due to changed field IDs.

Priority 6: User Communication and Training

Quick Win -- 1 to 2 hours

Send a migration summary email to all users explaining what changed, what stayed the same, and where to report issues.
Create a short FAQ document covering common questions: "Why do I see two fields with similar names?" and "Which field should I use for X?"
Schedule a 15-minute team demo showing the new Cloud interface, any changed workflows, and updated field behavior.
Set up a dedicated feedback channel (Slack channel, email alias, or Jira service project) for migration-related issues during the first two weeks.
Monitor the feedback channel daily and triage issues. Most early complaints are about missing fields or broken workflows -- address these within 24 hours.

Recommended Order of Operations

The order above is intentional. Here's why you should follow it:

Fields first. Duplicate fields affect everything downstream -- workflows, automation rules, dashboards. Fix the foundation before building on top of it.
Permissions second. Before you start reconfiguring workflows and automation, make sure the right people can actually access what they need.
Workflows and screens third. These depend on fields being correct. Once field cleanup is done, audit configurations with confidence.
Automation fourth. Automation rules reference specific fields and workflows. Rebuild them after both are stable.
Dashboards and reporting fifth. Reports depend on fields, workflows, and automation being correct. Fix upstream issues first.
User communication throughout. Start communicating early and continue through the entire cleanup process. Transparency reduces support tickets.

Common Post-Migration Mistakes to Avoid

Mistake 1: Skipping field cleanup and configuring new fields immediately. This creates a cascading problem. JCMA may create "(migrated)" copies of your new fields on the next migration run, doubling your cleanup workload.

Critical rule: Complete all duplicate field cleanup before adding new custom fields to Cloud. This is the single most important sequencing decision you'll make.

Mistake 2: Assuming JCMA migrated everything. JCMA is thorough but not perfect. Automation rules, webhooks, and some project-specific configurations often need manual recreation in Cloud.

Mistake 3: Not testing with real users before declaring the migration complete. Admin-level testing misses edge cases. Have actual end-users perform their daily tasks and report issues.

When to Consider Professional Help

If your instance has more than 100 custom fields, over 50k issues, or complex multi-project workflows with dozens of automation rules, the cleanup checklist above could take a full week or more. In these cases:

Use Migration Field Cleanup for Jira to automate the field portion (scan, classify, merge) -- this alone can save 2-3 days of manual work.
Hire an Atlassian Solution Partner for the workflow, automation, and configuration audit if your team lacks Cloud expertise.
Run a phased cleanup -- tackle the highest-impact projects first, then work through lower-priority ones over 2-3 weeks.

Resources

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