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A compromised GitHub repository should be treated as both a security incident and a source-control problem. Preserve evidence before deleting anything, contain access and execution, revoke or rotate every potentially exposed credential, then choose between restoring trusted references and rewriting history. Rewriting is not the default: it is justified when secrets or other sensitive files must be removed from historical objects.
The safest recovery order
Do not begin with a force-push or by deleting the suspicious commit. Those actions can destroy evidence and make the incident harder to scope. Use this order instead:
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- Preserve evidence and build a UTC timeline. Capture audit events, workflow runs, logs, suspicious commits, pull requests, ref changes, webhooks, keys, apps, runners and visibility changes before cleanup.
- Contain access and execution. Revoke known-compromised sessions and tokens, stop malicious automation, remove unauthorized persistence and limit further writes.
- Scope the incident. Establish the last known-good references and determine whether the attacker changed source code, CI/CD, credentials, repository settings or connected cloud systems.
- Rotate credentials and fix the entry point. Treat secrets exposed in code, logs, artifacts, clones, forks and pull requests as usable until revoked or replaced.
- Choose restoration or history rewriting. Restore or revert when the problem is an unauthorized current change. Rewrite only when sensitive data must disappear from historical refs.
- Coordinate every copy and validate the result. Existing clones, forks, pull requests and caches can retain old objects after a rewrite.
Keep an untouched evidence copy separate from the working repository. Never use that copy for cleanup commands.
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Preserve evidence before destructive cleanup
GitHub’s audit and automation records are time-sensitive. Opening a support ticket does not preserve logs or extend their retention period. Capture what you can before deleting branches, canceling runs or force-updating refs.
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Capture the repository state
- Record the repository URL, visibility, default branch, all branches and tags, and the UTC time of collection.
- Save suspicious commit IDs, parent IDs, tree contents, changed files and commit metadata.
- Export pull requests, reviews, comments, release assets and any references to the suspicious objects.
- Record force-pushes, branch-protection changes, repository transfers and visibility changes.
- Save workflow definitions, run histories, logs, artifacts and changes to workflow permissions.
Capture access and persistence indicators
- Organization and repository audit events, collaborator and team changes, SSO authorizations and installed GitHub Apps.
- Personal access tokens, deploy keys, SSH keys, environment-protection changes and deployment credentials that were added, removed or modified.
- Self-hosted runner registrations, labels, recent jobs and machine identities.
- Webhooks, delivery history, destination URLs and secret changes.
- Indicators of access to package registries, cloud accounts, signing systems or other external services through GitHub secrets.
Build a defensible timeline
For every event, record the UTC timestamp, actor identity, affected repository or organization, ref or object hash, action taken and the evidence file that supports it. Hash or otherwise protect collected files so later investigators can identify changes. Keep the original export read-only and perform analysis on copies.
Contain access, workflows and persistence
Containment should match the incident’s scope and the availability you must preserve. Start with controls that stop further abuse without destroying evidence.
Lock down identities and integrations
- Revoke known-compromised personal access tokens, OAuth or app authorizations, active sessions, deploy keys and SSH credentials.
- Review organization owners, repository administrators, collaborators, teams and SSO grants. Remove accounts or grants that were not authorized.
- Disable or remove unfamiliar GitHub Apps, webhooks and integrations. Preserve their configuration and delivery records first.
- Temporarily restrict repository writes or require additional review while the incident is being scoped.
Stop malicious execution
- Cancel suspicious workflow runs and disable Actions temporarily if jobs could continue exfiltrating secrets or changing refs.
- Remove unknown self-hosted runners and investigate the machines that hosted them before re-registering anything.
- Disable webhooks that can trigger external systems or receive repository data.
- Delete a branch containing malicious code or workflows only after its evidence has been captured and only when deleting it is necessary for containment.
A clean-looking default branch does not establish that an account, runner, webhook, app or cloud environment is safe. Treat each execution path as a separate trust decision.
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Scope what the attacker could reach
Find the last known-good branch and tag, then compare every current ref with that point. Include refs that are not shown in the normal day-to-day workflow: release tags, maintenance branches, pull-request refs and branches created during the incident.
Inspect source and delivery changes
- Review recent commits, amended commits, force-pushes and changes to workflow files.
- Check pull requests, reviews, merge events, release assets and generated artifacts for unauthorized content or embedded credentials.
- Look for persistence such as scheduled workflows, unexpected permissions, modified build scripts, altered deployment destinations or newly trusted branches.
- Compare branch-protection rules, required reviews, status checks and Actions permissions with the documented baseline.
Inspect the surrounding control plane
- Review audit-log events for collaborators, teams, apps, keys, runners, webhooks and repository visibility.
- Check whether workflow logs, artifacts, pull requests, forks or clones could have exposed secrets.
- Determine whether GitHub credentials were used to access cloud accounts, package registries, deployment targets or signing services.
- Record evidence of data exfiltration separately from evidence of code modification; a repository can be altered without proving that every secret was read, but possible exposure still requires rotation.
Do not delete suspicious objects while scoping them. Preserve the original refs and use copies or exported data for comparison.
Rotate every potentially exposed credential
Revocation or rotation comes before history rewriting. GitHub’s guidance notes that when the problem is a secret, rotating it may be sufficient and avoids the additional risks of rewriting. A secret that remains valid can be abused even after its text is removed from the visible branch.
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Credentials to review
- Repository and environment secrets, organization secrets and variables.
- Personal access tokens, OAuth or app credentials, deploy keys and SSH keys.
- Cloud access keys, deployment identities, container or package-registry tokens and signing keys.
- Credentials used by external integrations, webhooks, CI runners and release tooling.
- Any password, token or private key present in source, workflow output, an artifact, a pull request, a clone or a fork.
Make rotation effective
- Revoke the old credential first when the provider supports immediate revocation.
- Issue a replacement with the minimum required scope and an owner and expiration policy.
- Update every consumer, including deployment systems and local automation, then test from a trusted environment.
- Search logs, artifacts, caches and external systems for additional copies and rotate those credentials too.
- Patch or isolate the workstation, runner or integration that supplied the compromised access. Otherwise a new credential can be stolen again.
Choose between restoring history and rewriting it
Preserving commit history does not always mean preserving every object. Decide based on whether sensitive material must be removed, not on how unpleasant the malicious commit looks.
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|---|---|---|---|
| Revert the unauthorized change or restore trusted refs | Existing commits and hashes remain intact | The malicious change is contained, credentials are rotated, and no secret or sensitive file must be expunged | The unwanted or sensitive objects remain reachable in history |
Rewrite with git-filter-repo |
The legitimate narrative is retained, but the affected commit and every descendant receive new hashes | Secrets or sensitive files must be removed from all relevant refs | Recontamination, lost work, invalid signatures, clone and fork divergence, and substantial coordination |
When a revert is enough
After containment and rotation, restore a trusted branch or create a revert for an unauthorized current change when the historical content is not sensitive. This keeps existing clones and signatures coherent. Document the incident and the reason the original object remains, because a revert removes behavior from the current line but does not erase the earlier commit.
When rewriting is justified
Rewrite when a password, token, private key or sensitive file exists in history and must be removed from every relevant ref. Rotate or revoke it first. Rewriting before rotation creates a false sense of safety while old clones, logs or external systems may still contain a usable credential.
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Rewrite sensitive history with a clean copy
Use a fresh clone or a dedicated clean copy, not a clone that has been used for incident response or may contain untrusted hooks and objects. Install a current git-filter-repo release that supports the sensitive-data-removal workflow.
Remove a file from every relevant ref
GitHub documents this pattern for a file that must be removed throughout the repository:
git clone https://github.com/OWNER/REPOSITORY
cd REPOSITORY
git-filter-repo --sensitive-data-removal --invert-paths --path PATH-TO-FILEReplace the repository and path values with the actual target. If the file was moved or renamed, include every historical path. The command changes the commit containing the file and all descendants; it is not limited to the current branch.
Audit before publishing the rewrite
- List branches and tags and confirm that the intended refs, and only those refs, were rewritten.
- Search the rewritten object database and reachable history for the sensitive path, known secret values and related file names.
- Inspect the working tree, build output and tests from the rewritten state.
- Check generated files, release assets, submodules and large-file references for copies of the removed material.
- Review commit signatures and note which signatures are no longer valid because commit IDs changed.
- Have the incident owner approve the exact ref update and force-update plan before pushing.
Publish only the approved refs
A coordinated force update replaces remote references; it does not guarantee that every old object disappears. Push only the branches and tags included in the cleanup plan, communicate the maintenance window and keep the pre-rewrite evidence copy offline. Do not casually force-push all refs when only one branch was affected.
Coordinate clones, forks, pull requests and caches
Every clone made before the rewrite can retain the old objects. Forks, pull-request references, cached views and large-file storage can also preserve copies. A remote branch that looks clean therefore cannot prove that sensitive data is gone.
Give collaborators an explicit procedure
- Tell collaborators to preserve any required incident evidence before deleting or cleaning their clone.
- For ordinary development clones, the safest approach is to archive the old clone as evidence if needed and re-clone the rewritten repository.
- If a clone contains unpushed work, have its owner export that work, verify it does not include tainted objects, and reapply it to the rewritten base.
- Do not merge a branch created from tainted history. Rebase or recreate it from the cleaned refs so removed commits are not reintroduced.
- Ask fork owners to clean or delete affected forks. A fork outside your organization may require its owner’s cooperation.
Handle GitHub-held remnants
After local and remote cleanup, identify sensitive content still visible through cached pages, pull-request references or other server-side remnants and open a support request with the evidence and affected object IDs. GitHub Support does not remove ordinary non-sensitive data merely because a repository owner wants a cleaner history.
Validate the recovered repository before reopening development
Validation should prove both that the malicious state is gone and that the trusted workflow still works.
Security checks
- Confirm that malicious branches, tags, workflow files, webhooks, runners, keys, apps and access grants are removed or explicitly approved.
- Verify that every potentially exposed credential was revoked or replaced and that replacement credentials have narrower permissions.
- Restore branch protection, required reviews, status checks and environment approvals.
- Minimize Actions permissions, review workflow tokens and prevent untrusted pull requests from receiving unnecessary secrets.
- Enable or review secret-scanning and other available monitoring, then investigate Dependabot and malware alerts where available.
Functional checks
- Build and test from the trusted branch using a clean runner.
- Run deployment checks against a controlled environment before production.
- Confirm that release tags, artifacts, package publishing and rollback procedures point to the intended commits.
- Verify that collaborators can clone the cleaned refs and that no automated job recreates deleted branches or files.
Close the incident deliberately
Document the timeline, indicators, affected credentials, containment decisions, cleanup commands, rewritten refs, collaborator notifications and residual risk. Record why you chose a revert or a rewrite and retain the untouched evidence copy according to your incident-retention requirements.
Common recovery mistakes
- Force-pushing first: destroys useful evidence and leaves credentials valid.
- Deleting only the visible malicious commit: misses copies in other branches, tags, pull requests, forks, artifacts or logs.
- Rotating only the token named in the commit: overlooks environment, organization, app, deploy, cloud and signing credentials.
- Trusting a clean default branch: ignores runners, webhooks, apps, account access and external systems.
- Keeping old clones in circulation: lets removed commits and secrets be pushed back into the repository.
- Merging old feature branches after a rewrite: reintroduces the objects the rewrite removed.
- Assuming support will extend retention: logs can expire while a ticket is open.
- Rewriting without coordination: invalidates hashes and signatures and can discard collaborators’ work.
What “recovered” should mean
Recovery is complete when the entry point is fixed, credentials are no longer usable, malicious execution and persistence are removed, the chosen refs are verified, and every person or system that can write to the repository has moved to the trusted state. A revert preserves the original graph but leaves old objects reachable; a rewrite removes selected historical content from the published refs but creates new identities and requires coordinated cleanup. Choose the least disruptive option that actually removes the risk.
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