diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index 631fc7fb16..9013ab11f7 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -53,6 +53,11 @@ jobs:
     runs-on: [runs-on,runner=8cpu-linux-x64,image=ubuntu24-full-x64,"run-id=${{ github.run_id }}",spot=false,extras=s3-cache]
     container:
       image: ghcr.io/px4/px4-dev:v1.17.0-rc2
+    permissions:
+      contents: write
+    env:
+      GIT_COMMITTER_EMAIL: bot@px4.io
+      GIT_COMMITTER_NAME: PX4BuildBot
     steps:
       - uses: runs-on/action@v2
       - uses: actions/checkout@v6
@@ -76,3 +81,19 @@ jobs:
         if: always()
         with:
           cache-primary-key: ${{ steps.ccache.outputs.cache-primary-key }}
+
+      - name: Auto-update EKF change indication baselines
+        if: github.event_name == 'push'
+        uses: stefanzweifel/git-auto-commit-action@v7
+        with:
+          file_pattern: 'src/modules/ekf2/test/change_indication/*.csv'
+          commit_user_name: ${{ env.GIT_COMMITTER_NAME }}
+          commit_user_email: ${{ env.GIT_COMMITTER_EMAIL }}
+          commit_message: |
+            [AUTO COMMIT] update EKF change indication
+
+            See .github/workflows/checks.yml for more details
+
+      - name: Check for EKF functional changes
+        run: git diff --exit-code
+        working-directory: src/modules/ekf2/test/change_indication
diff --git a/.github/workflows/ekf_functional_change_indicator.yml b/.github/workflows/ekf_functional_change_indicator.yml
deleted file mode 100644
index 7feb0531bb..0000000000
--- a/.github/workflows/ekf_functional_change_indicator.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: EKF Change Indicator
-
-on:
-  pull_request:
-    branches:
-      - '**'
-    paths-ignore:
-      - 'docs/**'
-
-# If two events are triggered within a short time in the same PR, cancel the run of the oldest event
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
-  cancel-in-progress: true
-
-jobs:
-  unit_tests:
-    runs-on: ubuntu-latest
-
-    container:
-      image: ghcr.io/px4/px4-dev:v1.17.0-rc2
-
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: main test
-        run: |
-          cd "$GITHUB_WORKSPACE"
-          git config --system --add safe.directory '*'
-          make tests TESTFILTER=EKF
-
-      - name: Check if there is a functional change
-        run: git diff --exit-code
-        working-directory: src/modules/ekf2/test/change_indication
diff --git a/.github/workflows/ekf_update_change_indicator.yml b/.github/workflows/ekf_update_change_indicator.yml
deleted file mode 100644
index b01af805b6..0000000000
--- a/.github/workflows/ekf_update_change_indicator.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-name: EKF Update Change Indicator
-
-on:
-  push:
-    paths-ignore:
-      - 'docs/**'
-
-jobs:
-  unit_tests:
-    runs-on: ubuntu-latest
-
-    container:
-      image: ghcr.io/px4/px4-dev:v1.17.0-rc2
-
-    env:
-      GIT_COMMITTER_EMAIL: bot@px4.io
-      GIT_COMMITTER_NAME: PX4BuildBot
-
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: main test
-        run: |
-          cd "$GITHUB_WORKSPACE"
-          git config --system --add safe.directory '*'
-          make tests TESTFILTER=EKF
-
-      - name: Check if there exists diff and save result in variable
-        id: diff-check
-        working-directory: src/modules/ekf2/test/change_indication
-        run: |
-          if git diff --quiet; then
-            echo "CHANGE_INDICATED=false" >> $GITHUB_OUTPUT
-          else
-            echo "CHANGE_INDICATED=true" >> $GITHUB_OUTPUT
-          fi
-
-      - name: auto-commit any changes to change indication
-        if: steps.diff-check.outputs.CHANGE_INDICATED == 'true'
-        uses: stefanzweifel/git-auto-commit-action@v7
-        with:
-          file_pattern: 'src/modules/ekf2/test/change_indication/*.csv'
-          commit_user_name: ${{ env.GIT_COMMITTER_NAME }}
-          commit_user_email: ${{ env.GIT_COMMITTER_EMAIL }}
-          commit_message: |
-            [AUTO COMMIT] update change indication
-
-            See .github/workflows/ekf_update_change_indicator.yml for more details
-
-      - name: if there is a functional change, fail check
-        if: steps.diff-check.outputs.CHANGE_INDICATED == 'true'
-        run: exit 1