diff --git a/CHANGELOG.md b/CHANGELOG.md
index 07463f8f65..66a77dd299 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,8 @@
 
 ### Template
 
+- switch to uv and prek for pipeline linting workflow ([#3942](https://github.com/nf-core/tools/pull/3942))
+
 ### Linting
 
 - fix test for linting for version.yml ([#3947](https://github.com/nf-core/tools/pull/3947))
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index cc14b6c955..78083609c5 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -13,16 +13,8 @@ jobs:
     steps:
       - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1.0.11
 
   nf-core:
     runs-on: ubuntu-latest
@@ -38,6 +30,9 @@ jobs:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
@@ -45,9 +40,7 @@ jobs:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
         if: ${{ github.base_ref != 'master' }}