diff --git a/packages/e2e/setup/app.ts b/packages/e2e/setup/app.ts
index 7073b38a395..1053c96d8e8 100644
--- a/packages/e2e/setup/app.ts
+++ b/packages/e2e/setup/app.ts
@@ -2,7 +2,6 @@
 import {authFixture} from './auth.js'
 import {getLastPageStatus, isVisibleWithin, navigateToDashboard, refreshIfPageError} from './browser.js'
 import {CLI_TIMEOUT, BROWSER_TIMEOUT} from './constants.js'
-import {updateTomlValues} from '@shopify/toml-patch'
 import * as toml from '@iarna/toml'
 import * as path from 'path'
 import * as fs from 'fs'
@@ -112,17 +111,41 @@ export function extractClientId(appDir: string): string {
 }
 
 /**
- * Overwrite a created app's shopify.app.toml with a fixture TOML template.
- * Uses toml-patch to surgically set client_id and name while
- * preserving comments and formatting in the fixture file.
+ * Merge an E2E TOML fixture into the app config generated by the template.
+ * Template-owned fields not mentioned by the fixture are preserved.
  */
+type TomlTable = Parameters<typeof toml.stringify>[0]
+
+function isTomlTable(value: unknown): value is TomlTable {
+  return typeof value === 'object' && value !== null && !Array.isArray(value) && !(value instanceof Date)
+}
+
+function mergeTomlTables(base: TomlTable, overlay: TomlTable): TomlTable {
+  const merged: TomlTable = {...base}
+  for (const [key, overlayValue] of Object.entries(overlay)) {
+    const baseValue = merged[key]
+    merged[key] =
+      isTomlTable(baseValue) && isTomlTable(overlayValue) ? mergeTomlTables(baseValue, overlayValue) : overlayValue
+  }
+  return merged
+}
+
+export function mergeFixtureToml(generatedTomlContent: string, fixtureTomlContent: string, name: string): string {
+  const generated = toml.parse(generatedTomlContent)
+  const clientId = generated.client_id as string | undefined
+  if (!clientId) {
+    throw new Error('Could not find client_id in generated shopify.app.toml')
+  }
+
+  const fixture = toml.parse(fixtureTomlContent)
+
+  return toml.stringify(mergeTomlTables(generated, {...fixture, client_id: clientId, name}))
+}
+
 export function injectFixtureToml(appDir: string, fixtureTomlContent: string, name: string): void {
-  const clientId = extractClientId(appDir)
-  const patched = updateTomlValues(fixtureTomlContent, [
-    [['client_id'], clientId],
-    [['name'], name],
-  ])
-  fs.writeFileSync(path.join(appDir, 'shopify.app.toml'), patched)
+  const tomlPath = path.join(appDir, 'shopify.app.toml')
+  const patched = mergeFixtureToml(fs.readFileSync(tomlPath, 'utf8'), fixtureTomlContent, name)
+  fs.writeFileSync(tomlPath, patched)
 }
 
 export async function generateExtension(
diff --git a/packages/e2e/tests/fixture-toml.spec.ts b/packages/e2e/tests/fixture-toml.spec.ts
new file mode 100644
index 00000000000..e28ba61b40d
--- /dev/null
+++ b/packages/e2e/tests/fixture-toml.spec.ts
@@ -0,0 +1,79 @@
+/* eslint-disable no-restricted-imports */
+import {mergeFixtureToml} from '../setup/app.js'
+import {expect, test} from '@playwright/test'
+import * as toml from '@iarna/toml'
+import * as fs from 'fs'
+import * as path from 'path'
+import {fileURLToPath} from 'url'
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url))
+const VALID_APP_FIXTURE = fs.readFileSync(path.join(__dirname, '../data/valid-app/shopify.app.toml'), 'utf8')
+
+test.describe('fixture TOML', () => {
+  test('merges fixture values without dropping template-owned fields', () => {
+    const generatedToml = `
+client_id = "generated-client-id"
+name = "Generated app name"
+application_url = "https://template.example.com"
+
+[access_scopes]
+scopes = "read_products"
+
+[sidekick]
+extensions_summary = "Template-provided Sidekick summary"
+template_owned = true
+`.trimStart()
+
+    const fixtureToml = `
+client_id = "placeholder"
+name = "placeholder"
+application_url = "https://fixture.example.com"
+
+[build]
+include_config_on_deploy = true
+
+[sidekick]
+extensions_summary = "Fixture-provided Sidekick summary"
+`.trimStart()
+
+    const mergedToml = mergeFixtureToml(generatedToml, fixtureToml, 'E2E merged app')
+    const parsed = toml.parse(mergedToml)
+
+    expect(parsed.client_id).toBe('generated-client-id')
+    expect(parsed.name).toBe('E2E merged app')
+    expect(parsed.application_url).toBe('https://fixture.example.com')
+    expect(parsed.access_scopes).toEqual({scopes: 'read_products'})
+    expect(parsed.sidekick).toEqual({
+      extensions_summary: 'Fixture-provided Sidekick summary',
+      template_owned: true,
+    })
+    expect(parsed.build).toEqual({include_config_on_deploy: true})
+  })
+
+  test('valid app fixture can merge into generated template TOML', () => {
+    const generatedToml = `
+client_id = "generated-client-id"
+name = "Generated app name"
+
+[sidekick]
+extensions_summary = "Template-provided Sidekick summary"
+template_owned = true
+
+[template_owned]
+kept = true
+`.trimStart()
+
+    const mergedToml = mergeFixtureToml(generatedToml, VALID_APP_FIXTURE, 'E2E valid fixture app')
+    const parsed = toml.parse(mergedToml)
+
+    expect(parsed.client_id).toBe('generated-client-id')
+    expect(parsed.name).toBe('E2E valid fixture app')
+    expect(parsed.template_owned).toEqual({kept: true})
+    expect(parsed.sidekick).toEqual({
+      extensions_summary: 'Read, create, and edit FAQ entries stored in the app',
+      template_owned: true,
+    })
+    expect(parsed.webhooks).toMatchObject({api_version: '2025-01'})
+    expect((parsed.webhooks as {subscriptions: unknown[]}).subscriptions).toHaveLength(2)
+  })
+})