diff --git a/.changeset/eighty-ads-enjoy.md b/.changeset/eighty-ads-enjoy.md
new file mode 100644
index 0000000000..2d7084bb5b
--- /dev/null
+++ b/.changeset/eighty-ads-enjoy.md
@@ -0,0 +1,5 @@
+---
+'@shopify/app': patch
+---
+
+Fix redirect_urls being appended instead of replaced during app dev
diff --git a/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts b/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts
index 87d0eedabf..cfefd43a2a 100644
--- a/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts
+++ b/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts
@@ -8,6 +8,7 @@ import {describe, expect, test} from 'vitest'
 const defaultToml = `# Learn more about configuring your app at https://shopify.dev/docs/apps/tools/cli/configuration
 client_id = "12345"
 name = "app1"
+application_url = "https://example.com"
 embedded = true
 
 [access_scopes]
@@ -42,6 +43,9 @@ describe('patchAppConfigurationFile', () => {
         access_scopes: {
           use_legacy_install_flow: false,
         },
+        auth: {
+          redirect_urls: ['https://example.com/redirect3', 'https://example.com/redirect4'],
+        },
       }
 
       await patchAppConfigurationFile({path: configPath, patch, schema})
@@ -61,8 +65,8 @@ use_legacy_install_flow = false
 
 [auth]
 redirect_urls = [
-  "https://example.com/redirect",
-  "https://example.com/redirect2"
+  "https://example.com/redirect3",
+  "https://example.com/redirect4"
 ]
 
 [webhooks]
@@ -92,9 +96,6 @@ name = "app1"
 application_url = "https://example.com"
 embedded = true
 
-[build]
-dev_store_url = "example.myshopify.com"
-
 [access_scopes]
 # Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
 use_legacy_install_flow = true
@@ -107,6 +108,9 @@ redirect_urls = [
 
 [webhooks]
 api_version = "2023-04"
+
+[build]
+dev_store_url = "example.myshopify.com"
 `)
     })
   })
@@ -134,8 +138,8 @@ embedded = true
 
 [access_scopes]
 # Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
-scopes = "read_products"
 use_legacy_install_flow = true
+scopes = "read_products"
 
 [auth]
 redirect_urls = [
diff --git a/packages/app/src/cli/services/app/patch-app-configuration-file.ts b/packages/app/src/cli/services/app/patch-app-configuration-file.ts
index 5bb533407b..dc07a8d627 100644
--- a/packages/app/src/cli/services/app/patch-app-configuration-file.ts
+++ b/packages/app/src/cli/services/app/patch-app-configuration-file.ts
@@ -22,14 +22,18 @@ export interface PatchTomlOptions {
 export async function patchAppConfigurationFile({path, patch, schema}: PatchTomlOptions) {
   const tomlContents = await readFile(path)
   const configuration = decodeToml(tomlContents)
-  const updatedConfig = deepMergeObjects(configuration, patch)
+  const updatedConfig = deepMergeObjects(configuration, patch, replaceArrayStrategy)
 
   // Re-parse the config with the schema to validate the patch and keep the same order in the file
   // Make every field optional to not crash on invalid tomls that are missing fields.
   const validSchema = schema ?? zod.object({}).passthrough()
-  const validatedConfig = validSchema.partial().parse(updatedConfig)
-  let encodedString = encodeToml(validatedConfig)
+  validSchema.partial().parse(updatedConfig)
 
+  let encodedString = encodeToml(updatedConfig)
   encodedString = addDefaultCommentsToToml(encodedString)
   await writeFile(path, encodedString)
 }
+
+function replaceArrayStrategy(_: unknown[], sourceArray: unknown[]): unknown[] {
+  return sourceArray
+}