diff --git a/.changeset/theme-check-respect-user-config.md b/.changeset/theme-check-respect-user-config.md
new file mode 100644
index 0000000000..6107588da4
--- /dev/null
+++ b/.changeset/theme-check-respect-user-config.md
@@ -0,0 +1,5 @@
+---
+'@shopify/app': patch
+---
+
+`runThemeCheck` now respects a user's `.theme-check.yml` in the theme app extension root. When present, theme-check-node auto-discovery is used; otherwise the bundled `theme-check:theme-app-extension` config is applied as before. This lets extensions ignore source directories (e.g. a `src/` folder containing uncompiled Liquid templates) without forking the CLI.
diff --git a/packages/app/src/cli/services/build/theme-check.ts b/packages/app/src/cli/services/build/theme-check.ts
index 53a00faebd..5fcbb8b3fe 100644
--- a/packages/app/src/cli/services/build/theme-check.ts
+++ b/packages/app/src/cli/services/build/theme-check.ts
@@ -1,4 +1,5 @@
-import {readFileSync} from '@shopify/cli-kit/node/fs'
+import {fileExists, readFileSync} from '@shopify/cli-kit/node/fs'
+import {joinPath} from '@shopify/cli-kit/node/path'
 import {itemToString} from '@shopify/cli-kit/node/output'
 import {TokenItem} from '@shopify/cli-kit/node/ui'
 import {Severity, type Offense, check, path as pathUtils} from '@shopify/theme-check-node'
@@ -60,7 +61,11 @@ function formatOffenses(offenses: Offense[]): TokenItem {
 }
 
 export async function runThemeCheck(directory: string): Promise<string> {
-  const configPath = 'theme-check:theme-app-extension'
+  // Respect a user's `.theme-check.yml` in the extension root when present.
+  // Falling through to `undefined` lets theme-check-node auto-discover the
+  // user config; otherwise use the bundled theme-app-extension defaults.
+  const hasUserConfig = await fileExists(joinPath(directory, '.theme-check.yml'))
+  const configPath = hasUserConfig ? undefined : 'theme-check:theme-app-extension'
   const offenses = await check(directory, configPath)
   const formattedOffenses = formatOffenses(offenses)
   return itemToString(formattedOffenses)