diff --git a/.jules/tester.md b/.jules/tester.md
new file mode 100644
index 0000000000..144d2c3339
--- /dev/null
+++ b/.jules/tester.md
@@ -0,0 +1,7 @@
+## 2025-05-15 - Remove filesystem mocks in execute-command-helpers.test.ts
+
+**Gap**: Tests for `prepareExecuteContext` were using `vi.mock('@shopify/cli-kit/node/fs')` to mock `readFile` and `fileExists`, which only verifies that the functions were called with expected arguments rather than verifying the actual behavior of reading and validating GraphQL query files.
+
+**Learning**: Using `inTemporaryDirectory` and `writeFile` from `@shopify/cli-kit/node/fs` allows for more robust testing of logic that depends on the filesystem. It also prevents "false pass" scenarios where the mock might not perfectly reflect real filesystem behavior (e.g., handling of empty files or whitespace).
+
+**Action**: Refactored `packages/app/src/cli/utilities/execute-command-helpers.test.ts` to remove the global `fs` mock and use real temporary directories.
diff --git a/packages/app/src/cli/utilities/execute-command-helpers.test.ts b/packages/app/src/cli/utilities/execute-command-helpers.test.ts
index 5d31edc237..73031df740 100644
--- a/packages/app/src/cli/utilities/execute-command-helpers.test.ts
+++ b/packages/app/src/cli/utilities/execute-command-helpers.test.ts
@@ -2,12 +2,12 @@ import {prepareAppStoreContext, prepareExecuteContext} from './execute-command-h
 import {linkedAppContext} from '../services/app-context.js'
 import {storeContext} from '../services/store-context.js'
 import {validateSingleOperation} from '../services/graphql/common.js'
-import {readFile, fileExists} from '@shopify/cli-kit/node/fs'
+import {inTemporaryDirectory, writeFile} from '@shopify/cli-kit/node/fs'
+import {joinPath} from '@shopify/cli-kit/node/path'
 import {describe, test, expect, vi, beforeEach} from 'vitest'
 
 vi.mock('../services/app-context.js')
 vi.mock('../services/store-context.js')
-vi.mock('@shopify/cli-kit/node/fs')
 vi.mock('@shopify/cli-kit/node/system')
 vi.mock('../services/graphql/common.js', () => ({
   validateSingleOperation: vi.fn(),
@@ -160,43 +160,55 @@ describe('prepareExecuteContext', () => {
   })
 
   test('reads query from file when query-file flag is provided', async () => {
-    const queryFileContent = 'query { shop { name } }'
-    vi.mocked(fileExists).mockResolvedValue(true)
-    vi.mocked(readFile).mockResolvedValue(queryFileContent as any)
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const queryFileContent = 'query { shop { name } }'
+      const queryFilePath = joinPath(tmpDir, 'query.graphql')
+      await writeFile(queryFilePath, queryFileContent)
 
-    const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': '/path/to/query.graphql'}
-    const result = await prepareExecuteContext(flagsWithQueryFile)
+      const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': queryFilePath}
 
-    expect(fileExists).toHaveBeenCalledWith('/path/to/query.graphql')
-    expect(readFile).toHaveBeenCalledWith('/path/to/query.graphql', {encoding: 'utf8'})
-    expect(result.query).toBe(queryFileContent)
+      // When
+      const result = await prepareExecuteContext(flagsWithQueryFile)
+
+      // Then
+      expect(result.query).toBe(queryFileContent)
+    })
   })
 
   test('throws AbortError when query file does not exist', async () => {
-    vi.mocked(fileExists).mockResolvedValue(false)
-
-    const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': '/path/to/nonexistent.graphql'}
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const queryFilePath = joinPath(tmpDir, 'nonexistent.graphql')
+      const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': queryFilePath}
 
-    await expect(prepareExecuteContext(flagsWithQueryFile)).rejects.toThrow('Query file not found')
-    expect(readFile).not.toHaveBeenCalled()
+      // When/Then
+      await expect(prepareExecuteContext(flagsWithQueryFile)).rejects.toThrow('Query file not found')
+    })
   })
 
   test('throws AbortError when query file is empty', async () => {
-    vi.mocked(fileExists).mockResolvedValue(true)
-    vi.mocked(readFile).mockResolvedValue('' as any)
-
-    const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': '/path/to/empty.graphql'}
-
-    await expect(prepareExecuteContext(flagsWithQueryFile)).rejects.toThrow('is empty')
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const queryFilePath = joinPath(tmpDir, 'empty.graphql')
+      await writeFile(queryFilePath, '')
+      const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': queryFilePath}
+
+      // When/Then
+      await expect(prepareExecuteContext(flagsWithQueryFile)).rejects.toThrow('is empty')
+    })
   })
 
   test('throws AbortError when query file contains only whitespace', async () => {
-    vi.mocked(fileExists).mockResolvedValue(true)
-    vi.mocked(readFile).mockResolvedValue('   \n\t  ' as any)
-
-    const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': '/path/to/whitespace.graphql'}
-
-    await expect(prepareExecuteContext(flagsWithQueryFile)).rejects.toThrow('is empty')
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given
+      const queryFilePath = joinPath(tmpDir, 'whitespace.graphql')
+      await writeFile(queryFilePath, '   \n\t  ')
+      const flagsWithQueryFile = {...mockFlags, query: undefined, 'query-file': queryFilePath}
+
+      // When/Then
+      await expect(prepareExecuteContext(flagsWithQueryFile)).rejects.toThrow('is empty')
+    })
   })
 
   test('validates GraphQL query using validateSingleOperation', async () => {