diff --git a/.changeset/function-prepare-variables-check.md b/.changeset/function-prepare-variables-check.md
new file mode 100644
index 00000000000..4bff7ecb163
--- /dev/null
+++ b/.changeset/function-prepare-variables-check.md
@@ -0,0 +1,6 @@
+---
+'@shopify/app': minor
+'@shopify/cli': minor
+---
+
+Run `@shopify/shopify_function`'s `check.js`, when the package has it, before building a JavaScript function. It fails the build when a prepare target returns variables its run target's input query doesn't accept.
diff --git a/packages/app/src/cli/services/function/build.test.ts b/packages/app/src/cli/services/function/build.test.ts
index c1bebcd99cd..457b029bb95 100644
--- a/packages/app/src/cli/services/function/build.test.ts
+++ b/packages/app/src/cli/services/function/build.test.ts
@@ -7,6 +7,7 @@ import {
   runWasmOpt,
   runTrampoline,
   buildJSFunction,
+  checkJSFunction,
 } from './build.js'
 import {
   javyBinary,
@@ -479,6 +480,98 @@ describe('bundleExtension', () => {
   })
 })
 
+describe('checkJSFunction', () => {
+  const config = {
+    name: 'test function',
+    type: 'function',
+    build: {wasm_opt: true},
+    configuration_ui: false,
+    api_version: '2026-07',
+    targeting: [
+      {target: 'cart.validations.generate.prepare', export: 'cart-validations-generate-prepare'},
+      {
+        target: 'cart.validations.generate.run',
+        input_query: 'src/run.graphql',
+        export: 'cart-validations-generate-run',
+      },
+    ],
+  }
+
+  async function installCheck(tmpDir: string) {
+    const check = joinPath(tmpDir, 'node_modules/@shopify/shopify_function/check.js')
+    await mkdir(dirname(check))
+    await writeFile(check, '')
+    return check
+  }
+
+  test("runs @shopify/shopify_function's check.js with the function's targets", async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const ourFunction = await testFunctionExtension({dir: tmpDir, entryPath: 'src/index.js', config})
+      const check = await installCheck(tmpDir)
+      let functionJson: unknown
+      vi.mocked(exec).mockImplementation(async (_command, args) => {
+        functionJson = JSON.parse(await readFile(args.at(-1)!))
+      })
+
+      // When
+      await checkJSFunction(ourFunction, {stdout, stderr, signal, app})
+
+      // Then
+      expect(exec).toHaveBeenCalledWith(
+        process.execPath,
+        [check, '--function', expect.stringMatching(/function\.json$/)],
+        {cwd: tmpDir, stderr, signal},
+      )
+      expect(functionJson).toEqual({
+        handle: ourFunction.handle,
+        directory: tmpDir,
+        entry: 'src/index.js',
+        schema: joinPath(tmpDir, 'schema.graphql'),
+        targets: [
+          {target: 'cart.validations.generate.prepare', export: 'cartValidationsGeneratePrepare'},
+          {
+            target: 'cart.validations.generate.run',
+            export: 'cartValidationsGenerateRun',
+            inputQuery: joinPath(tmpDir, 'src/run.graphql'),
+          },
+        ],
+      })
+    })
+  })
+
+  test('does nothing when @shopify/shopify_function has no check.js', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const ourFunction = await testFunctionExtension({dir: tmpDir, entryPath: 'src/index.js', config})
+
+      // When
+      await checkJSFunction(ourFunction, {stdout, stderr, signal, app})
+
+      // Then
+      expect(exec).not.toHaveBeenCalled()
+    })
+  })
+
+  test('fails the build when the check fails', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const ourFunction = await testFunctionExtension({dir: tmpDir, entryPath: 'src/index.js', config})
+      await installShopifyLibrary(tmpDir)
+      const check = await installCheck(tmpDir)
+      vi.mocked(exec).mockRejectedValueOnce(new Error('prepare variables mismatch'))
+
+      // When
+      const got = buildJSFunction(ourFunction, {stdout, stderr, signal, app})
+
+      // Then
+      await expect(got).rejects.toThrow('prepare variables mismatch')
+      expect(exec).toHaveBeenCalledTimes(1)
+      expect(exec).toHaveBeenCalledWith(process.execPath, [check, '--function', expect.any(String)], expect.anything())
+    })
+  })
+})
+
 describe('runJavy', () => {
   test('captures compiler diagnostics in the dev session log in text mode', async () => {
     const {exec: execute} =
diff --git a/packages/app/src/cli/services/function/build.ts b/packages/app/src/cli/services/function/build.ts
index 57d09db0137..b4f24a7f69f 100644
--- a/packages/app/src/cli/services/function/build.ts
+++ b/packages/app/src/cli/services/function/build.ts
@@ -94,6 +94,7 @@ export async function buildJSFunction(fun: ExtensionInstance<FunctionConfigType>
   const javyBuilder: JavyBuilder = exports.length === 0 ? DefaultJavyBuilder : new ExportJavyBuilder(exports)
 
   const deps = await validateShopifyFunctionPackageVersion(fun)
+  await checkJSFunction(fun, options)
 
   if (options.useTasks) {
     return buildJSFunctionWithTasks(fun, options, javyBuilder, deps)
@@ -102,6 +103,36 @@ export async function buildJSFunction(fun: ExtensionInstance<FunctionConfigType>
   }
 }
 
+// Runs @shopify/shopify_function's check.js, when the package has it, before the function is built.
+export async function checkJSFunction(fun: ExtensionInstance<FunctionConfigType>, options: JSFunctionBuildOptions) {
+  const check = await findPathUp('node_modules/@shopify/shopify_function/check.js', {type: 'file', cwd: fun.directory})
+  if (!check) return
+
+  await inTemporaryDirectory(async (temporaryDirectory) => {
+    // Each target's export is the function the bundle imports for it
+    const functionPath = joinPath(temporaryDirectory, 'function.json')
+    await writeFile(
+      functionPath,
+      JSON.stringify({
+        handle: fun.handle,
+        directory: fun.directory,
+        entry: fun.entrySourceFilePath,
+        schema: joinPath(fun.directory, 'schema.graphql'),
+        targets: (fun.configuration.targeting ?? []).map((targeting) => ({
+          target: targeting.target,
+          export: targeting.export && camelize(targeting.export),
+          inputQuery: targeting.input_query && joinPath(fun.directory, targeting.input_query),
+        })),
+      }),
+    )
+    await exec(process.execPath, [check, '--function', functionPath], {
+      cwd: fun.directory,
+      stderr: options.stderr,
+      signal: options.signal,
+    })
+  })
+}
+
 async function buildJSFunctionWithoutTasks(
   fun: ExtensionInstance<FunctionConfigType>,
   options: JSFunctionBuildOptions,