diff --git a/.github/workflows/preprocessing-nextclade.yml b/.github/workflows/preprocessing-nextclade.yml
index 5575f8f51..4dffa1609 100644
--- a/.github/workflows/preprocessing-nextclade.yml
+++ b/.github/workflows/preprocessing-nextclade.yml
@@ -12,8 +12,7 @@ on:
 
 env:
   DOCKER_IMAGE_NAME: ghcr.io/loculus-project/preprocessing-nextclade
-  # BUILD_ARM: ${{ github.ref == 'refs/heads/main' || github.event.inputs.build_arm }} # Uncomment once nextclade in bioconda aarch64
-  BUILD_ARM: ${{ github.event.inputs.build_arm }}
+  BUILD_ARM: ${{ github.ref == 'refs/heads/main' || github.event.inputs.build_arm }}
 
 concurrency:
   group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-preprocessing-nextclade
diff --git a/preprocessing/nextclade/environment.yml b/preprocessing/nextclade/environment.yml
index b291dece1..027d1e3b2 100644
--- a/preprocessing/nextclade/environment.yml
+++ b/preprocessing/nextclade/environment.yml
@@ -5,8 +5,8 @@ channels:
 dependencies:
   - python=3.12
   - biopython=1.83
-  - nextclade=3.2.1
+  - nextclade=3.3.1
   - PyYAML
   - requests=2.31
   - pyjwt=2.8
-  - pip
\ No newline at end of file
+  - pip