diff --git a/packages/vite/src/node/config.ts b/packages/vite/src/node/config.ts
index 8f16aed9c84917..d6b32d4a52ada5 100644
--- a/packages/vite/src/node/config.ts
+++ b/packages/vite/src/node/config.ts
@@ -427,6 +427,15 @@ export async function resolveConfig(
     }
   }
 
+  if (process.env.VITE_TEST_WITHOUT_PLUGIN_COMMONJS) {
+    config = mergeConfig(config, {
+      optimizeDeps: { disabled: false },
+      ssr: { optimizeDeps: { disabled: false } }
+    })
+    config.build ??= {}
+    config.build.commonjsOptions = { include: [] }
+  }
+
   // resolve root
   const resolvedRoot = normalizePath(
     config.root ? path.resolve(config.root) : process.cwd()
@@ -563,16 +572,6 @@ export async function resolveConfig(
 
   const optimizeDeps = config.optimizeDeps || {}
 
-  if (process.env.VITE_TEST_WITHOUT_PLUGIN_COMMONJS) {
-    config.build ??= {}
-    config.build.commonjsOptions = { include: [] }
-    config.optimizeDeps ??= {}
-    config.optimizeDeps.disabled = false
-    config.ssr ??= {}
-    config.ssr.optimizeDeps ??= {}
-    config.ssr.optimizeDeps.disabled = false
-  }
-
   const BASE_URL = resolvedBase
 
   const resolved: ResolvedConfig = {