diff --git a/.github/workflows/pathogen-repo-build.yaml b/.github/workflows/pathogen-repo-build.yaml
index 2109a7d..ef31dfc 100644
--- a/.github/workflows/pathogen-repo-build.yaml
+++ b/.github/workflows/pathogen-repo-build.yaml
@@ -349,7 +349,7 @@ jobs:
           "$NEXTSTRAIN_GITHUB_DIR"/bin/interpolate-env < "$NEXTSTRAIN_GITHUB_DIR"/text-templates/attach-aws-batch.md \
           > "$GITHUB_STEP_SUMMARY"
       - if: always()
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           if-no-files-found: warn
           name: ${{ inputs.artifact-name }}
diff --git a/.github/workflows/pathogen-repo-build.yaml.in b/.github/workflows/pathogen-repo-build.yaml.in
index 01d0343..9849f8d 100644
--- a/.github/workflows/pathogen-repo-build.yaml.in
+++ b/.github/workflows/pathogen-repo-build.yaml.in
@@ -330,7 +330,7 @@ jobs:
           > "$GITHUB_STEP_SUMMARY"
 
       - if: always()
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           if-no-files-found: warn
           name: ${{ inputs.artifact-name }}
diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index ecf6201..29c3b49 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -295,7 +295,7 @@ jobs:
         id: nextclade
         run: nextstrain build nextclade --configfile build-configs/ci/config.yaml
       - if: always()
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
           if-no-files-found: ignore
diff --git a/.github/workflows/pathogen-repo-ci.yaml.in b/.github/workflows/pathogen-repo-ci.yaml.in
index 7ee6153..35c0dbe 100644
--- a/.github/workflows/pathogen-repo-ci.yaml.in
+++ b/.github/workflows/pathogen-repo-ci.yaml.in
@@ -275,7 +275,7 @@ jobs:
         run: nextstrain build nextclade --configfile build-configs/ci/config.yaml
 
       - if: always()
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
           if-no-files-found: ignore