diff --git a/CHANGELOG.md b/CHANGELOG.md
index b36802c145..d7e1afb421 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@
 - Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
 - Improve test coverage of sync.py
 - `check_up_to_date()` function from `modules_json` also checks for subworkflows.
+- The default branch can now be specified when creating a new pipeline repo [#1959](https://github.com/nf-core/tools/pull/1959).
 
 ### Modules
 
diff --git a/nf_core/create.py b/nf_core/create.py
index 457adc3266..bd00dd1517 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -40,6 +40,8 @@ class PipelineCreate(object):
             May the force be with you.
         outdir (str): Path to the local output directory.
         template_yaml (str): Path to template.yml file for pipeline creation settings.
+        plain (bool): If true the Git repository will be initialized plain.
+        default_branch (str): Specifies the --initial-branch name.
     """
 
     def __init__(
@@ -53,6 +55,7 @@ def __init__(
         outdir=None,
         template_yaml_path=None,
         plain=False,
+        default_branch=None,
     ):
         self.template_params, skip_paths_keys = self.create_param_dict(
             name, description, author, version, template_yaml_path, plain
@@ -82,6 +85,7 @@ def __init__(
         self.no_git = (
             no_git if self.template_params["github"] else True
         )  # Set to True if template was configured without github hosting
+        self.default_branch = default_branch
         self.force = force
         if outdir is None:
             outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
@@ -528,24 +532,27 @@ def git_init_pipeline(self):
         Raises:
             UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
         """
-        # Check that the default branch is not dev
+        default_branch = self.default_branch
         try:
-            default_branch = git.config.GitConfigParser().get_value("init", "defaultBranch")
+            default_branch = default_branch or git.config.GitConfigParser().get_value("init", "defaultBranch")
         except configparser.Error:
-            default_branch = None
             log.debug("Could not read init.defaultBranch")
-        if default_branch == "dev" or default_branch == "TEMPLATE":
+        if default_branch in ["dev", "TEMPLATE"]:
             raise UserWarning(
-                f"Your Git defaultBranch is set to '{default_branch}', which is incompatible with nf-core.\n"
-                "This can be modified with the command [white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
-                "Pipeline git repository is not initialised."
+                f"Your Git defaultBranch '{default_branch}' is incompatible with nf-core.\n"
+                "'dev' and 'TEMPLATE' can not be used as default branch name.\n"
+                "Set the default branch name with "
+                "[white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
+                "Or set the default_branch parameter in this class.\n"
+                "Pipeline git repository will not be initialised."
             )
-        # Initialise pipeline
+
         log.info("Initialising pipeline git repository")
         repo = git.Repo.init(self.outdir)
+        if default_branch:
+            repo.active_branch.rename(default_branch)
         repo.git.add(A=True)
         repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
-        # Add TEMPLATE branch to git repository
         repo.git.branch("TEMPLATE")
         repo.git.branch("dev")
         log.info(
diff --git a/tests/test_create.py b/tests/test_create.py
index 5f8f6546f2..5f732fc180 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -4,6 +4,8 @@
 import os
 import unittest
 
+import git
+
 import nf_core.create
 
 from .utils import with_temporary_folder
@@ -16,6 +18,7 @@ def setUp(self, tmp_path):
         self.pipeline_description = "just for 4w3s0m3 tests"
         self.pipeline_author = "Chuck Norris"
         self.pipeline_version = "1.0.0"
+        self.default_branch = "default"
 
         self.pipeline = nf_core.create.PipelineCreate(
             name=self.pipeline_name,
@@ -26,6 +29,7 @@ def setUp(self, tmp_path):
             force=True,
             outdir=tmp_path,
             plain=True,
+            default_branch=self.default_branch,
         )
 
     def test_pipeline_creation(self):
@@ -37,3 +41,4 @@ def test_pipeline_creation(self):
     def test_pipeline_creation_initiation(self):
         self.pipeline.init_pipeline()
         assert os.path.isdir(os.path.join(self.pipeline.outdir, ".git"))
+        assert f" {self.default_branch}\n" in git.Repo.init(self.pipeline.outdir).git.branch()
diff --git a/tests/test_sync.py b/tests/test_sync.py
index 075690b2c0..0cedf51698 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -26,12 +26,14 @@ def setUp(self):
         """Create a new pipeline to test"""
         self.tmp_dir = tempfile.mkdtemp()
         self.pipeline_dir = os.path.join(self.tmp_dir, "testpipeline")
+        default_branch = "master"
         self.create_obj = nf_core.create.PipelineCreate(
-            "testing", "test pipeline", "tester", outdir=self.pipeline_dir, plain=True
+            "testing", "test pipeline", "tester", outdir=self.pipeline_dir, plain=True, default_branch=default_branch
         )
         self.create_obj.init_pipeline()
         self.remote_path = os.path.join(self.tmp_dir, "remote_repo")
         self.remote_repo = git.Repo.init(self.remote_path, bare=True)
+        self.remote_repo.active_branch.rename(default_branch)
 
     def tearDown(self):
         if os.path.exists(self.tmp_dir):