diff --git a/packages/gatsby/src/schema/graphql-engine/print-plugins.ts b/packages/gatsby/src/schema/graphql-engine/print-plugins.ts
index 154e70fc7fbe7..dae57fc47c49d 100644
--- a/packages/gatsby/src/schema/graphql-engine/print-plugins.ts
+++ b/packages/gatsby/src/schema/graphql-engine/print-plugins.ts
@@ -7,7 +7,7 @@ import { store } from "../../redux"
 import { IGatsbyState } from "../../redux/types"
 import { requireGatsbyPlugin } from "../../utils/require-gatsby-plugin"
 
-const schemaCustomizationAPIs = new Set([
+export const schemaCustomizationAPIs = new Set([
   `setFieldsOnGraphQLNodeType`,
   `createSchemaCustomization`,
   `createResolvers`,
@@ -73,7 +73,7 @@ function render(
   const imports: Array<string> = [
     ...uniqGatsbyNode.map(
       (plugin, i) =>
-        `import * as pluginGatsbyNode${i} from "${relativePluginPath(
+        `import * as pluginGatsbyNode${i} from "gatsby/dist/schema/graphql-engine/webpack-remove-apis-loader!${relativePluginPath(
           plugin.resolve
         )}/gatsby-node"`
     ),
diff --git a/packages/gatsby/src/schema/graphql-engine/webpack-remove-apis-loader.ts b/packages/gatsby/src/schema/graphql-engine/webpack-remove-apis-loader.ts
new file mode 100644
index 0000000000000..638ece7fe78c3
--- /dev/null
+++ b/packages/gatsby/src/schema/graphql-engine/webpack-remove-apis-loader.ts
@@ -0,0 +1,23 @@
+import { transformSync } from "@babel/core"
+import { GatsbyNodeAPI } from "../../redux/types"
+import * as nodeApis from "../../utils/api-node-docs"
+import { schemaCustomizationAPIs } from "./print-plugins"
+
+module.exports = function loader(source: string): string | null | undefined {
+  const result = transformSync(source, {
+    babelrc: false,
+    configFile: false,
+    plugins: [
+      [
+        require.resolve(`../../utils/babel/babel-plugin-remove-api`),
+        {
+          apis: (Object.keys(nodeApis) as Array<GatsbyNodeAPI>).filter(
+            api => !schemaCustomizationAPIs.has(api)
+          ),
+        },
+      ],
+    ],
+  })
+
+  return result?.code
+}