diff --git a/.github/workflows/pathogen-repo-build.yaml b/.github/workflows/pathogen-repo-build.yaml
index c6b2da1..4f57bbb 100644
--- a/.github/workflows/pathogen-repo-build.yaml
+++ b/.github/workflows/pathogen-repo-build.yaml
@@ -276,7 +276,7 @@ jobs:
           # shellcheck disable=SC2154
           set -x
 
-          eval "unbuffer $NEXTSTRAIN_BUILD_COMMAND" |& tee build.log
+          eval "unbuffer $NEXTSTRAIN_BUILD_COMMAND" |& tee -a build.log
       # Attempt to get the AWS Batch ID even if the run build command failed
       # as long as the runtime is `aws-batch` and the `build.log` file exists
       - if: ${{ always() && inputs.runtime == 'aws-batch' && hashFiles('build.log') != '' }}
diff --git a/.github/workflows/pathogen-repo-build.yaml.in b/.github/workflows/pathogen-repo-build.yaml.in
index 54f548a..d218586 100644
--- a/.github/workflows/pathogen-repo-build.yaml.in
+++ b/.github/workflows/pathogen-repo-build.yaml.in
@@ -243,7 +243,7 @@ jobs:
           # shellcheck disable=SC2154
           set -x
 
-          eval "unbuffer $NEXTSTRAIN_BUILD_COMMAND" |& tee build.log
+          eval "unbuffer $NEXTSTRAIN_BUILD_COMMAND" |& tee -a build.log
 
       # Attempt to get the AWS Batch ID even if the run build command failed
       # as long as the runtime is `aws-batch` and the `build.log` file exists