diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index f16612954..005964519 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -87,9 +87,6 @@ jobs:
           - { pathogen: avian-flu, build-args: auspice/flu_avian_h5n1_ha.json }
           - { pathogen: ebola }
           - { pathogen: lassa }
-          # Disable mpox CI until pathogen-repo-ci supports custom build directories
-          # See issue https://github.com/nextstrain/.github/issues/63
-          # - { pathogen: mpox }
           - { pathogen: mumps }
           - {
               pathogen: ncov,
@@ -101,7 +98,12 @@ jobs:
               build-args: --configfile profiles/ci/builds.yaml -p,
             }
           - { pathogen: tb }
-          - { pathogen: zika }
+
+          # Disable some pathogens until pathogen-repo-ci supports custom build directories
+          # See issue https://github.com/nextstrain/.github/issues/63
+          # - { pathogen: mpox }
+          # - { pathogen: zika }
+
     name: pathogen-repo-ci (${{ matrix.pathogen }})
     defaults:
       run: