diff --git a/.github/workflows/pathogen-repo-build.yaml b/.github/workflows/pathogen-repo-build.yaml
index a3a418d..966ef97 100644
--- a/.github/workflows/pathogen-repo-build.yaml
+++ b/.github/workflows/pathogen-repo-build.yaml
@@ -47,12 +47,17 @@ on:
 
           If your build runs longer than the 6 hour limit for a single GitHub Action job, then use the aws-batch runtime and the `--detach` flag. Subsequent chained jobs will be automatically used to wait on the remote build for up to 24 hours total.
 
-          All environment variables provided via the env input and all secrets provided via `secrets: inherit` can be passed to the build runtime via the `--env` option.  If AWS credentials were acquired by the GitHub Action job via role assumption, the following environment variables are also available to be passed:
+          All environment variables provided via the env input and all secrets provided via `secrets: inherit` can be passed to the build runtime via the `--env` option.
 
+          It is assumed that the pathogen repo build requires AWS credentials for read/write access to S3 buckets. These may come directly from secrets or indirectly from assuming a role via GitHub Actions' OIDC provider.
 
-            - AWS_ACCESS_KEY_ID
-            - AWS_SECRET_ACCESS_KEY
-            - AWS_SESSION_TOKEN
+          The following secrets are used if present:
+
+          - AWS_ACCESS_KEY_ID - AWS_SECRET_ACCESS_KEY
+
+          They must be defined in the repo's Actions secrets and passed to this workflow with `secrets: inherit`.
+
+          If no secrets are present, the GitHubActionsRoleNextstrainS3Access role is assumed (in both senses of the verb) with additional repo specific inline session policies defined in text-templates/repo-aws-iam-policy.json
         type: string
         default: nextstrain build .
         required: false
@@ -138,12 +143,17 @@ on:
 
           If your build runs longer than the 6 hour limit for a single GitHub Action job, then use the aws-batch runtime and the `--detach` flag. Subsequent chained jobs will be automatically used to wait on the remote build for up to 24 hours total.
 
-          All environment variables provided via the env input and all secrets provided via `secrets: inherit` can be passed to the build runtime via the `--env` option.  If AWS credentials were acquired by the GitHub Action job via role assumption, the following environment variables are also available to be passed:
+          All environment variables provided via the env input and all secrets provided via `secrets: inherit` can be passed to the build runtime via the `--env` option.
+
+          It is assumed that the pathogen repo build requires AWS credentials for read/write access to S3 buckets. These may come directly from secrets or indirectly from assuming a role via GitHub Actions' OIDC provider.
+
+          The following secrets are used if present:
+
+          - AWS_ACCESS_KEY_ID - AWS_SECRET_ACCESS_KEY
 
+          They must be defined in the repo's Actions secrets and passed to this workflow with `secrets: inherit`.
 
-            - AWS_ACCESS_KEY_ID
-            - AWS_SECRET_ACCESS_KEY
-            - AWS_SESSION_TOKEN
+          If no secrets are present, the GitHubActionsRoleNextstrainS3Access role is assumed (in both senses of the verb) with additional repo specific inline session policies defined in text-templates/repo-aws-iam-policy.json
         type: string
         default: nextstrain build .
         required: false
@@ -210,6 +220,7 @@ on:
 env:
   NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
   NEXTSTRAIN_BUILD_LOG: build.log
+  NEXTSTRAIN_RUNTIME_ENVDIR: .git/nextstrain/env.d
 permissions:
   id-token: write
 jobs:
@@ -255,6 +266,30 @@ jobs:
 
           echo "$secrets" | jq 'del(.github_token)' | "$NEXTSTRAIN_GITHUB_DIR"/bin/json-to-envvars | tee -a "$GITHUB_ENV"
 
+      - id: role
+        name: Set repo-specific role to (potentially) assume for runtime access to AWS
+        env:
+          REPO_FULL_NAME: ${{ inputs.repo }}
+        run: |
+          echo "arn=arn:aws:iam::827581582529:role/GitHubActionsRoleNextstrainRepo@${REPO_FULL_NAME#*/}" | tee -a "$GITHUB_OUTPUT"
+      - uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-region: us-east-1
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          role-to-assume: ${{ secrets.AWS_ACCESS_KEY_ID == '' && steps.role.outputs.arn || '' }}
+          role-duration-seconds: 43200 # seconds, or 12 hours
+      - name: Save runtime AWS credentials to ${{ env.NEXTSTRAIN_RUNTIME_ENVDIR }}
+        run: |
+          ./bin/write-envdir "$NEXTSTRAIN_RUNTIME_ENVDIR" \
+            AWS_ACCESS_KEY_ID \
+            AWS_SECRET_ACCESS_KEY \
+            AWS_SESSION_TOKEN
+        # This will overwrite the runtime AWS credential envvars configured above
+        # so if the build is using the aws-batch runtime, the Nextstrain CLI will
+        # have access to the AWS Batch session credentials
+        # Comment only applies to this first use of the `&setup-aws-batch-credentials`, so
+        # outdenting comments to not repeat it with expanded YAML
       - if: inputs.runtime == 'aws-batch'
         uses: aws-actions/configure-aws-credentials@v4
         with:
@@ -271,6 +306,7 @@ jobs:
       - name: Run build via ${{ inputs.runtime }}
         env:
           NEXTSTRAIN_BUILD_COMMAND: ${{ inputs.run }}
+          NEXTSTRAIN_RUNTIME_ENVDIRS: ${{ env.NEXTSTRAIN_RUNTIME_ENVDIR }}
         run: |
           # shellcheck disable=SC2154
           set -x
diff --git a/.github/workflows/pathogen-repo-build.yaml.in b/.github/workflows/pathogen-repo-build.yaml.in
index 315ffe8..df5afae 100644
--- a/.github/workflows/pathogen-repo-build.yaml.in
+++ b/.github/workflows/pathogen-repo-build.yaml.in
@@ -66,13 +66,23 @@ on:
 
           All environment variables provided via the env input and all secrets
           provided via `secrets: inherit` can be passed to the build runtime
-          via the `--env` option.  If AWS credentials were acquired by the
-          GitHub Action job via role assumption, the following environment
-          variables are also available to be passed:
+          via the `--env` option.
 
-            - AWS_ACCESS_KEY_ID
-            - AWS_SECRET_ACCESS_KEY
-            - AWS_SESSION_TOKEN
+          It is assumed that the pathogen repo build requires AWS credentials for
+          read/write access to S3 buckets. These may come directly from secrets
+          or indirectly from assuming a role via GitHub Actions' OIDC provider.
+
+          The following secrets are used if present:
+
+          - AWS_ACCESS_KEY_ID
+          - AWS_SECRET_ACCESS_KEY
+
+          They must be defined in the repo's Actions secrets and passed to this
+          workflow with `secrets: inherit`.
+
+          If no secrets are present, the GitHubActionsRoleNextstrainS3Access
+          role is assumed (in both senses of the verb) with additional repo specific
+          inline session policies defined in text-templates/repo-aws-iam-policy.json
         type: string
         default: nextstrain build .
         required: false
@@ -162,6 +172,7 @@ on:
 env:
   NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
   NEXTSTRAIN_BUILD_LOG: build.log
+  NEXTSTRAIN_RUNTIME_ENVDIR: .git/nextstrain/env.d
 
 permissions:
   id-token: write
@@ -218,6 +229,33 @@ jobs:
           | "$NEXTSTRAIN_GITHUB_DIR"/bin/json-to-envvars
           | tee -a "$GITHUB_ENV"
 
+      - id: role
+        name: Set repo-specific role to (potentially) assume for runtime access to AWS
+        env:
+          REPO_FULL_NAME: ${{ inputs.repo }}
+        run: |
+          echo "arn=arn:aws:iam::827581582529:role/GitHubActionsRoleNextstrainRepo@${REPO_FULL_NAME#*/}" | tee -a "$GITHUB_OUTPUT"
+
+      - uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-region: us-east-1
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          role-to-assume: ${{ secrets.AWS_ACCESS_KEY_ID == '' && steps.role.outputs.arn || '' }}
+          role-duration-seconds: 43200 # seconds, or 12 hours
+
+      - name: Save runtime AWS credentials to ${{ env.NEXTSTRAIN_RUNTIME_ENVDIR }}
+        run: |
+          ./bin/write-envdir "$NEXTSTRAIN_RUNTIME_ENVDIR" \
+            AWS_ACCESS_KEY_ID \
+            AWS_SECRET_ACCESS_KEY \
+            AWS_SESSION_TOKEN
+
+    # This will overwrite the runtime AWS credential envvars configured above
+    # so if the build is using the aws-batch runtime, the Nextstrain CLI will
+    # have access to the AWS Batch session credentials
+    # Comment only applies to this first use of the `&setup-aws-batch-credentials`, so
+    # outdenting comments to not repeat it with expanded YAML
       - &setup-aws-batch-credentials
         if: inputs.runtime == 'aws-batch'
         uses: aws-actions/configure-aws-credentials@v4
@@ -238,6 +276,7 @@ jobs:
       - name: Run build via ${{ inputs.runtime }}
         env:
           NEXTSTRAIN_BUILD_COMMAND: ${{ inputs.run }}
+          NEXTSTRAIN_RUNTIME_ENVDIRS: ${{ env.NEXTSTRAIN_RUNTIME_ENVDIR }}
         run: |
           # shellcheck disable=SC2154
           set -x