diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index bbb9f1a602..410196ac8f 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -114,6 +114,22 @@ jobs:
             exit 1
           fi
 
+      - name: Generate coverage XML
+        if: always()
+        run: |
+          uv run coverage xml --rcfile=.coveragerc
+
+      - name: Upload coverage to Codecov
+        if: always()
+        uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5
+        with:
+          files: ./coverage.xml
+          flags: python-${{ matrix.python-version }}
+          env_vars: MATRIX_TEST
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          MATRIX_TEST: ${{ matrix.test }}
+
       - name: remove slashes from test name
         run: |
           test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
@@ -126,47 +142,3 @@ jobs:
           include-hidden-files: true
           name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
-
-      - name: Upload coverage
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
-        with:
-          include-hidden-files: true
-          name: coverage_py${{ matrix.python-version }}_${{ env.test }}
-          path: .coverage
-
-  coverage:
-    needs: test
-    runs-on:
-      - runs-on=${{ github.run_id }}-coverage
-      - runner=2cpu-linux-x64
-    steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
-      - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install coverage
-        run: pip install coverage
-
-      - name: move coveragerc file up
-        run: |
-          mv .github/.coveragerc .
-
-      - name: Download all artifacts
-        uses: actions/download-artifact@018cc2cf5baa6db3ef3c5f8a56943fffe632ef53 # v6
-        with:
-          pattern: coverage_*
-
-      - name: Run coverage
-        run: |
-          coverage combine --keep coverage_*/.coverage*
-          coverage report
-          coverage xml
-
-      - uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5
-        with:
-          files: coverage.xml
-          disable_search: true # we already know the file to upload
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index dac1598d91..fe11ab2ef4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 - Switch from pre-commit to prek for pre-commit hooks in development([#3899](https://github.com/nf-core/tools/pull/3899))
 - 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))
+- Simplify coverage reporting in pytest.yml ([#3934](https://github.com/nf-core/tools/pull/3934))
 - add pre-commit hook to keep uv.lock in sync ([#3933](https://github.com/nf-core/tools/pull/3933))
 
 ### Template