diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 625f00d24..b0464d274 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -87,6 +87,14 @@ jobs:
         with:
           version: "latest-everything"
 
+      - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
+        run: |
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          if [ -z "$defaultBranch" ]; then
+            defaultBranch="master"
+          fi
+          git config --global init.defaultBranch $defaultBranch
+
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'
         env:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4eef49da4..73760131f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,7 @@
 - Don't break gitpod.yml with template string ([#3332](https://github.com/nf-core/tools/pull/3332))
 - rocrate: remove duplicated entries for name and version ([#3333](https://github.com/nf-core/tools/pull/3333))
 - rocrate: Update crate with version bump and handle new contributor field ([#3334](https://github.com/nf-core/tools/pull/3334))
+- Set git defaultBranch to master in sync action ([#3337](https://github.com/nf-core/tools/pull/3337))
 
 ### Version updates