diff --git a/.github/workflows/ci-linters.yml b/.github/workflows/ci-linters.yml
index de506b26b..3fa8b5025 100644
--- a/.github/workflows/ci-linters.yml
+++ b/.github/workflows/ci-linters.yml
@@ -10,10 +10,10 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout TileDB-VCF
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
index 8c6b70b2e..c7faadf07 100644
--- a/.github/workflows/macos.yml
+++ b/.github/workflows/macos.yml
@@ -20,7 +20,7 @@ jobs:
   libtiledbvcf:
     runs-on: macos-15
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Setup to build htslib from source
         run: brew install autoconf automake
       - name: Configure libtiledbvcf
@@ -69,7 +69,7 @@ jobs:
     env:
       DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/lib"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0 # fetch everything for python setuptools_scm
       - name: Download libtiledbvcf artifact
@@ -78,11 +78,11 @@ jobs:
           name: libtiledbvcf
           path: dist
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Install libtiledb
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: ci
           create-args: tiledb
@@ -101,7 +101,7 @@ jobs:
     runs-on: macos-15
     needs: libtiledbvcf
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Download libtiledbvcf artifact
         uses: actions/download-artifact@v4
         with:
@@ -116,13 +116,13 @@ jobs:
   python-standalone:
     runs-on: macos-15
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0 # fetch everything for python setuptools_scm
       - name: Setup to build htslib from source
         run: brew install autoconf automake
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Build tiledbvcf-py
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index ba042fb98..325302454 100644
--- a/.github/workflows/nightly.yml
+++ b/.github/workflows/nightly.yml
@@ -30,19 +30,19 @@ jobs:
       MACOSX_DEPLOYMENT_TARGET: 10.15
     steps:
       - name: Clone TileDB
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: TileDB-Inc/TileDB
           ref: ${{ matrix.branches.libtiledb }}
           path: TileDB
       - name: Clone TileDB-Py
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: TileDB-Inc/TileDB-Py
           ref: ${{ matrix.branches.tiledb-py }}
           path: TileDB-Py
       - name: Clone TileDB-VCF
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           path: TileDB-VCF
           fetch-depth: 0 # fetch everything for python setuptools_scm
@@ -80,7 +80,7 @@ jobs:
       - name: Test libtiledbvcf
         run: bash TileDB-VCF/ci/nightly/test-libtiledbvcf.sh
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Build tiledb-py from source
@@ -94,7 +94,7 @@ jobs:
     needs: nightly
     if: ( failure() || cancelled() ) && github.repository_owner == 'TileDB-Inc' && github.event_name == 'schedule'
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Open Issue
         uses: TileDB-Inc/github-actions/open-issue@main
         with:
diff --git a/.github/workflows/quarto-render.yml b/.github/workflows/quarto-render.yml
index 0f7757cc0..4b0af6ea5 100644
--- a/.github/workflows/quarto-render.yml
+++ b/.github/workflows/quarto-render.yml
@@ -9,7 +9,7 @@ jobs:
   quarto-render-and-deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: "Install Quarto"
       uses: quarto-dev/quarto-actions/setup@v2
@@ -25,7 +25,7 @@ jobs:
         # https://github.com/quarto-dev/quarto-cli/issues/493
 
     - name: "Deploy to gh-pages"
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       # Change to the name of your repo's primary branch name:
       if: github.ref == 'refs/heads/main' && github.repository_owner == 'TileDB-Inc'
       with:
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
index 40a3ae241..fc173275b 100644
--- a/.github/workflows/windows.yml
+++ b/.github/workflows/windows.yml
@@ -26,9 +26,9 @@ jobs:
   build:
     runs-on: windows-2022
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install conda env
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ci/gha-win-env.yml
           cache-environment: true