diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index bc1c848cd..2a6f8e8bf 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -277,24 +277,29 @@ def make_template_pipeline(self):
             with open(self.config_yml_path, "w") as config_path:
                 yaml.safe_dump(self.config_yml.model_dump(exclude_none=True), config_path)
 
-        pipeline_create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            outdir=str(self.pipeline_dir),
-            from_config_file=True,
-            no_git=True,
-            force=True,
-        )
-        pipeline_create_obj.init_pipeline()
-
-        # set force to false to avoid overwriting files in the future
-        if self.config_yml.template is not None:
-            self.config_yml.template = pipeline_create_obj.config
-            # Set force true in config to overwrite existing files
-            self.config_yml.template.force = False
-            # Set outdir as the current directory to avoid local info leaking
-            self.config_yml.template.outdir = "."
-            # Update nf-core version
-            self.config_yml.nf_core_version = nf_core.__version__
-            dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump(exclude_none=True))
+        try:
+            pipeline_create_obj = nf_core.pipelines.create.create.PipelineCreate(
+                outdir=str(self.pipeline_dir),
+                from_config_file=True,
+                no_git=True,
+                force=True,
+            )
+            pipeline_create_obj.init_pipeline()
+
+            # set force to false to avoid overwriting files in the future
+            if self.config_yml.template is not None:
+                self.config_yml.template = pipeline_create_obj.config
+                # Set force true in config to overwrite existing files
+                self.config_yml.template.force = False
+                # Set outdir as the current directory to avoid local info leaking
+                self.config_yml.template.outdir = "."
+                # Update nf-core version
+                self.config_yml.nf_core_version = nf_core.__version__
+                dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump(exclude_none=True))
+        except Exception as e:
+            # Reset to where you were to prevent git getting messed up.
+            self.repo.git.reset("--hard")
+            raise SyncExceptionError(f"Failed to rebuild pipeline from template with error:\n{e}")
 
     def commit_template_changes(self):
         """If we have any changes with the new template files, make a git commit"""