diff --git a/x-pack/plugins/fleet/server/services/epm/archive/parse.ts b/x-pack/plugins/fleet/server/services/epm/archive/parse.ts
index 1007b1fe35344..f071ba8bbfcc0 100644
--- a/x-pack/plugins/fleet/server/services/epm/archive/parse.ts
+++ b/x-pack/plugins/fleet/server/services/epm/archive/parse.ts
@@ -244,6 +244,11 @@ function parseAndVerifyArchive(paths: string[], topLevelDirOverride?: string): A
       semverPrerelease(parsed.version) || semverMajor(parsed.version) < 1 ? 'beta' : 'ga';
   }
 
+  // Ensure top-level variables are parsed as well
+  if (manifest.vars) {
+    parsed.vars = parseAndVerifyVars(manifest.vars, 'manifest.yml');
+  }
+
   return parsed;
 }