diff --git a/.github/workflows/ci_cmake.yml b/.github/workflows/ci_cmake.yml
index d709395c..379fbb28 100644
--- a/.github/workflows/ci_cmake.yml
+++ b/.github/workflows/ci_cmake.yml
@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/gcc-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: true
 
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
index 5df24c16..076ca6a1 100644
--- a/.github/workflows/ci_coverage.yml
+++ b/.github/workflows/ci_coverage.yml
@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
index 9a10894b..1cb7fec0 100644
--- a/.github/workflows/ci_documentation.yml
+++ b/.github/workflows/ci_documentation.yml
@@ -34,12 +34,12 @@ jobs:
     steps:
       - name: Checkout
         if: github.event_name != 'pull_request_target'
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       # pull_request_target does not checkout the merge commit by default
       - name: Checkout
         if: github.event_name == 'pull_request_target'
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: "refs/pull/${{ github.event.number }}/merge"
 
diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml
index afa46b39..1fc252f3 100644
--- a/.github/workflows/ci_license.yml
+++ b/.github/workflows/ci_license.yml
@@ -32,7 +32,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: REUSE Compliance Check
         uses: fsfe/reuse-action@v6
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
index 1aab08a9..6e7a5650 100644
--- a/.github/workflows/ci_linux.yml
+++ b/.github/workflows/ci_linux.yml
@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main
diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index 1c34d3ee..97bddfe4 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -36,7 +36,7 @@ jobs:
         compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
index 9e79a4b0..058af7bc 100644
--- a/.github/workflows/ci_misc.yml
+++ b/.github/workflows/ci_misc.yml
@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main
diff --git a/.github/workflows/cron_api.yml b/.github/workflows/cron_api.yml
index c9d20243..3b1349f8 100644
--- a/.github/workflows/cron_api.yml
+++ b/.github/workflows/cron_api.yml
@@ -37,7 +37,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: true
 
diff --git a/.github/workflows/cron_codeql.yml b/.github/workflows/cron_codeql.yml
index e4a16076..cf6a2e49 100644
--- a/.github/workflows/cron_codeql.yml
+++ b/.github/workflows/cron_codeql.yml
@@ -33,7 +33,7 @@ jobs:
       image: ghcr.io/seqan/gcc-second-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
 
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v4
diff --git a/.github/workflows/readme_snippet.yml b/.github/workflows/readme_snippet.yml
index 6e2bbfa6..262d9c1d 100644
--- a/.github/workflows/readme_snippet.yml
+++ b/.github/workflows/readme_snippet.yml
@@ -29,7 +29,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     steps:
       - name: Checkout Sharg
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           token: ${{ secrets.SEQAN_ACTIONS_PAT }}
 
diff --git a/.github/workflows/update_cookbook.yml b/.github/workflows/update_cookbook.yml
index 4d2f86b0..95f734e4 100644
--- a/.github/workflows/update_cookbook.yml
+++ b/.github/workflows/update_cookbook.yml
@@ -29,7 +29,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     steps:
       - name: Checkout Sharg
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           token: ${{ secrets.SEQAN_ACTIONS_PAT }}