diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index fa6c38ef07..0166c966ff 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -3,6 +3,8 @@ on:
   push:
     branches:
       - dev
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
     paths-ignore:
       - "docs/**"
       - "CHANGELOG.md"
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cabd4b9abe..a69c08ea52 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -3,6 +3,8 @@ on:
   push:
     branches:
       - dev
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
     paths:
       - nf_core/pipeline-template/**
   pull_request:
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 53f84b72c4..735cfebc36 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -3,6 +3,8 @@ on:
   push:
     branches:
       - dev
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
     paths-ignore:
       - "docs/**"
       - "CHANGELOG.md"
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 7ffd6e9df9..93de1cc154 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -3,6 +3,8 @@ on:
   push:
     branches:
       - dev
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
   pull_request:
   release:
     types: [published]
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 76d5d710c0..2b655e9393 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -5,6 +5,8 @@ on:
   push:
     branches:
       - dev
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
     paths-ignore:
       - "docs/**"
       - "CHANGELOG.md"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 603fa77e24..f3ef7e680d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -69,6 +69,7 @@
 - set default_branch to master for now ([#3335](https://github.com/nf-core/tools/issues/3335))
 - Set git defaultBranch to master in sync action ([#3337](https://github.com/nf-core/tools/pull/3337))
 - Add verbose mode to sync action ([#3339](https://github.com/nf-core/tools/pull/3339))
+- ci: Run checks on renovate branches to avoid creating and merging PRs ([#3018](https://github.com/nf-core/tools/pull/3018))
 
 ### Version updates