diff --git a/.changeset/remove-app-generate-schema-command.md b/.changeset/remove-app-generate-schema-command.md
new file mode 100644
index 00000000000..e107378be6e
--- /dev/null
+++ b/.changeset/remove-app-generate-schema-command.md
@@ -0,0 +1,5 @@
+---
+'@shopify/app': major
+---
+
+Remove the deprecated `shopify app generate schema` command. Use `shopify app function schema` instead.
diff --git a/packages/app/src/cli/commands/app/generate/schema.ts b/packages/app/src/cli/commands/app/generate/schema.ts
deleted file mode 100644
index 9189c2680c8..00000000000
--- a/packages/app/src/cli/commands/app/generate/schema.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-import FetchSchema from '../function/schema.js'
-
-export default class GenerateSchema extends FetchSchema {
-  static hidden = true
-
-  static descriptionWithMarkdown = `[DEPRECATED, use \`app function schema\`] Generates the latest [GraphQL schema](https://shopify.dev/docs/apps/functions/input-output#graphql-schema) for a function in your app. Run this command from the function directory.
-
-  This command uses the API type and version of your function, as defined in your extension TOML file, to generate the latest GraphQL schema. The schema is written to the \`schema.graphql\` file.`
-
-  static description = this.descriptionWithoutMarkdown()
-}
diff --git a/packages/app/src/cli/index.ts b/packages/app/src/cli/index.ts
index 6578cdb93a0..8ae694ad4b6 100644
--- a/packages/app/src/cli/index.ts
+++ b/packages/app/src/cli/index.ts
@@ -19,7 +19,6 @@ import FunctionRun from './commands/app/function/run.js'
 import FetchSchema from './commands/app/function/schema.js'
 import FunctionTypegen from './commands/app/function/typegen.js'
 import AppGenerateExtension from './commands/app/generate/extension.js'
-import GenerateSchema from './commands/app/generate/schema.js'
 import ImportExtensions from './commands/app/import-extensions.js'
 import AppInfo from './commands/app/info.js'
 import Init from './commands/app/init.js'
@@ -65,7 +64,6 @@ export const commands: {[key: string]: typeof AppLinkedCommand | typeof AppUnlin
   'app:env:show': EnvShow,
   'app:execute': Execute,
   'app:bulk:execute': BulkExecute,
-  'app:generate:schema': GenerateSchema,
   'app:function:build': FunctionBuild,
   'app:function:replay': FunctionReplay,
   'app:function:run': FunctionRun,
diff --git a/packages/cli/oclif.manifest.json b/packages/cli/oclif.manifest.json
index 7fd1048256e..ad9cfd500c8 100644
--- a/packages/cli/oclif.manifest.json
+++ b/packages/cli/oclif.manifest.json
@@ -2143,93 +2143,6 @@
       "strict": true,
       "summary": "Generate a new app Extension."
     },
-    "app:generate:schema": {
-      "aliases": [
-      ],
-      "args": {
-      },
-      "customPluginName": "@shopify/app",
-      "description": "\"DEPRECATED, use `app function schema`] Generates the latest [GraphQL schema\" (https://shopify.dev/docs/apps/functions/input-output#graphql-schema) for a function in your app. Run this command from the function directory.\n\n  This command uses the API type and version of your function, as defined in your extension TOML file, to generate the latest GraphQL schema. The schema is written to the `schema.graphql` file.",
-      "descriptionWithMarkdown": "[DEPRECATED, use `app function schema`] Generates the latest [GraphQL schema](https://shopify.dev/docs/apps/functions/input-output#graphql-schema) for a function in your app. Run this command from the function directory.\n\n  This command uses the API type and version of your function, as defined in your extension TOML file, to generate the latest GraphQL schema. The schema is written to the `schema.graphql` file.",
-      "flags": {
-        "client-id": {
-          "description": "The Client ID of your app.",
-          "env": "SHOPIFY_FLAG_CLIENT_ID",
-          "exclusive": [
-            "config"
-          ],
-          "hasDynamicHelp": false,
-          "hidden": false,
-          "multiple": false,
-          "name": "client-id",
-          "type": "option"
-        },
-        "config": {
-          "char": "c",
-          "description": "The name of the app configuration.",
-          "env": "SHOPIFY_FLAG_APP_CONFIG",
-          "hasDynamicHelp": false,
-          "hidden": false,
-          "multiple": false,
-          "name": "config",
-          "type": "option"
-        },
-        "no-color": {
-          "allowNo": false,
-          "description": "Disable color output.",
-          "env": "SHOPIFY_FLAG_NO_COLOR",
-          "hidden": false,
-          "name": "no-color",
-          "type": "boolean"
-        },
-        "path": {
-          "description": "The path to your function directory.",
-          "env": "SHOPIFY_FLAG_PATH",
-          "hasDynamicHelp": false,
-          "hidden": false,
-          "multiple": false,
-          "name": "path",
-          "noCacheDefault": true,
-          "type": "option"
-        },
-        "reset": {
-          "allowNo": false,
-          "description": "Reset all your settings.",
-          "env": "SHOPIFY_FLAG_RESET",
-          "exclusive": [
-            "config"
-          ],
-          "hidden": false,
-          "name": "reset",
-          "type": "boolean"
-        },
-        "stdout": {
-          "allowNo": false,
-          "description": "Output the schema to stdout instead of writing to a file.",
-          "env": "SHOPIFY_FLAG_STDOUT",
-          "name": "stdout",
-          "required": false,
-          "type": "boolean"
-        },
-        "verbose": {
-          "allowNo": false,
-          "description": "Increase the verbosity of the output.",
-          "env": "SHOPIFY_FLAG_VERBOSE",
-          "hidden": false,
-          "name": "verbose",
-          "type": "boolean"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hidden": true,
-      "hiddenAliases": [
-      ],
-      "id": "app:generate:schema",
-      "pluginAlias": "@shopify/cli",
-      "pluginName": "@shopify/cli",
-      "pluginType": "core",
-      "summary": "Fetch the latest GraphQL schema for a function."
-    },
     "app:import-custom-data-definitions": {
       "aliases": [
       ],