diff --git a/CHANGELOG.md b/CHANGELOG.md
index dac1598d91..6b93768805 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - switch to uv and pyproject.toml ([#3925](https://github.com/nf-core/tools/pull/3925))
 - Pin j178/prek-action action to 91fd7d7 ([#3931](https://github.com/nf-core/tools/pull/3931))
 - add pre-commit hook to keep uv.lock in sync ([#3933](https://github.com/nf-core/tools/pull/3933))
+- sync: don't overwrite the defaultBranch if already set in nextflow.config ([#3939](https://github.com/nf-core/tools/pull/3939))
 
 ### Template
 
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index bfc8a97efb..73885f2e21 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -94,8 +94,9 @@ def __init__(
         if self.config.outdir is None:
             self.config.outdir = str(Path.cwd())
 
-        # Get the default branch name from the Git configuration
-        self.get_default_branch()
+        # Get the default branch name from the Git configuration if it was not parsed from nextflow.config previously
+        if self.default_branch == "master":
+            self.get_default_branch()
 
         self.jinja_params, self.skip_areas = self.obtain_jinja_params_dict(
             self.config.skip_features or [], str(self.config.outdir)
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 7ce358cd07..f54dbe2d56 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -202,7 +202,7 @@ def inspect_sync_dir(self):
         # Track ignored files to avoid processing them
         self.ignored_files = self._get_ignored_files()
 
-    def get_wf_config(self):
+    def get_wf_config(self) -> None:
         """Check out the target branch if requested and fetch the nextflow config.
         Check that we have the required config variables.
         """
@@ -290,7 +290,7 @@ def _clean_up_empty_dirs(self):
                     raise SyncExceptionError(e)
                 deleted.add(Path(curr_dir))
 
-    def make_template_pipeline(self):
+    def make_template_pipeline(self) -> None:
         """
         Delete all files and make a fresh template using the workflow variables
         """
@@ -315,6 +315,7 @@ def make_template_pipeline(self):
                 from_config_file=True,
                 no_git=True,
                 force=True,
+                default_branch=self.wf_config.get("manifest.defaultBranch") or "master",
             )
             pipeline_create_obj.init_pipeline()