diff --git a/.changeset/witty-insects-study.md b/.changeset/witty-insects-study.md
new file mode 100644
index 00000000000..be233818522
--- /dev/null
+++ b/.changeset/witty-insects-study.md
@@ -0,0 +1,5 @@
+---
+'@shopify/theme': patch
+---
+
+Fix `shopify theme pull --only <value>` so it does not delete ignored files
diff --git a/packages/theme/src/cli/utilities/theme-downloader.test.ts b/packages/theme/src/cli/utilities/theme-downloader.test.ts
index d42cc8a8af7..e35c9d5118c 100644
--- a/packages/theme/src/cli/utilities/theme-downloader.test.ts
+++ b/packages/theme/src/cli/utilities/theme-downloader.test.ts
@@ -32,6 +32,26 @@ describe('theme-downloader', () => {
       expect(spy).toHaveBeenCalledWith('assets/deleteme.css')
     })
 
+    test('does not delete files when filters are passed', async () => {
+      // Given
+      const remote: Checksum[] = []
+      const files = new Map<string, ThemeAsset>([
+        ['assets/keepme.css', {key: 'assets/keepme.css', checksum: '1', value: 'content'}],
+      ])
+      const fileSystem = fakeThemeFileSystem(root, files, {
+        filters: {
+          only: ['templates/*'],
+        },
+      })
+      const spy = vi.spyOn(fileSystem, 'delete')
+
+      // When
+      await downloadTheme(remoteTheme, adminSession, remote, fileSystem, downloadOptions)
+
+      // Then
+      expect(spy).not.toHaveBeenCalled()
+    })
+
     test('does not delete files when nodelete is set', async () => {
       // Given
       const downloadOptions = {nodelete: true}
diff --git a/packages/theme/src/cli/utilities/theme-downloader.ts b/packages/theme/src/cli/utilities/theme-downloader.ts
index cb4e2e0a63a..85f082fc8a1 100644
--- a/packages/theme/src/cli/utilities/theme-downloader.ts
+++ b/packages/theme/src/cli/utilities/theme-downloader.ts
@@ -29,7 +29,7 @@ function buildDeleteTasks(remoteChecksums: Checksum[], themeFileSystem: ThemeFil
 
   const remoteKeys = new Set(remoteChecksums.map((checksum) => checksum.key))
 
-  const localKeys = Array.from(themeFileSystem.files.keys())
+  const localKeys = themeFileSystem.applyIgnoreFilters([...themeFileSystem.files.values()]).map(({key}) => key)
   const localFilesToBeDeleted = localKeys.filter((key) => !remoteKeys.has(key))
 
   return localFilesToBeDeleted.map((key) => {