diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95b7757c0..5b8483b01 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@
 
 - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
 - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226))
+- Remove unrelated values when saving `.nf-core` file ([#3227](https://github.com/nf-core/tools/pull/3227))
 - chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229))
 - Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232))
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 0b3c53f3a..16125aed3 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -19,7 +19,7 @@
 import time
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, Literal, Optional, Tuple, Union
 
 import git
 import prompt_toolkit.styles
@@ -1094,10 +1094,10 @@ def get(self, item: str, default: Any = None) -> Any:
 class NFCoreYamlConfig(BaseModel):
     """.nf-core.yml configuration file schema"""
 
-    repository_type: str
-    """ Type of repository: pipeline or modules """
+    repository_type: Optional[Literal["pipeline", "modules"]] = None
+    """ Type of repository """
     nf_core_version: Optional[str] = None
-    """ Version of nf-core/tools used to create/update the pipeline"""
+    """ Version of nf-core/tools used to create/update the pipeline """
     org_path: Optional[str] = None
     """ Path to the organisation's modules repository (used for modules repo_type only) """
     lint: Optional[LintConfigType] = None
@@ -1105,9 +1105,9 @@ class NFCoreYamlConfig(BaseModel):
     template: Optional[NFCoreTemplateConfig] = None
     """ Pipeline template configuration """
     bump_version: Optional[Dict[str, bool]] = None
-    """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information."""
+    """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information. """
     update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None
-    """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information."""
+    """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information. """
 
     def __getitem__(self, item: str) -> Any:
         return getattr(self, item)
@@ -1115,6 +1115,23 @@ def __getitem__(self, item: str) -> Any:
     def get(self, item: str, default: Any = None) -> Any:
         return getattr(self, item, default)
 
+    def model_dump(self, **kwargs) -> Dict[str, Any]:
+        # Get the initial data
+        config = super().model_dump(**kwargs)
+
+        if self.repository_type == "modules":
+            # Fields to exclude for modules
+            fields_to_exclude = ["template", "update"]
+        else:  # pipeline
+            # Fields to exclude for pipeline
+            fields_to_exclude = ["bump_version", "org_path"]
+
+        # Remove the fields based on repository_type
+        for field in fields_to_exclude:
+            config.pop(field, None)
+
+        return config
+
 
 def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path], Optional[NFCoreYamlConfig]]:
     """
diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py
index 955c00da8..b49b60436 100644
--- a/tests/pipelines/lint/test_nfcore_yml.py
+++ b/tests/pipelines/lint/test_nfcore_yml.py
@@ -33,7 +33,9 @@ def test_nfcore_yml_fail_repo_type(self):
         with open(self.nf_core_yml, "w") as fh:
             fh.write(new_content)
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
+        # assert that it raises assertion error
+        with self.assertRaises(AssertionError):
+            lint_obj._load()
         results = lint_obj.nfcore_yml()
         assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"])
         assert len(results.get("warned", [])) == 0