diff --git a/.changeset/pretty-vans-unite.md b/.changeset/pretty-vans-unite.md
index faf535c053..318e86d069 100644
--- a/.changeset/pretty-vans-unite.md
+++ b/.changeset/pretty-vans-unite.md
@@ -6,4 +6,6 @@ Package roles are now marked as stable and migration is encouraged. Please check
 
 The new `package`, `repo`, and `migrate` command categories are now marked as stable.
 
+Marked all commands that are being replaced by the new `package` and `repo` commands as deprecated.
+
 The package templates used by the `create` command have all been updated to use package roles.
diff --git a/packages/cli/src/commands/index.ts b/packages/cli/src/commands/index.ts
index 9b272fab95..bc427bb19b 100644
--- a/packages/cli/src/commands/index.ts
+++ b/packages/cli/src/commands/index.ts
@@ -172,7 +172,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('app:build')
-    .description('Build an app for a production release')
+    .description('Build an app for a production release [DEPRECATED]')
     .option('--stats', 'Write bundle stats to output directory')
     .option(...configOption)
     .action(lazy(() => import('./app/build').then(m => m.default)));
@@ -180,7 +180,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('app:serve')
-    .description('Serve an app for local development')
+    .description('Serve an app for local development [DEPRECATED]')
     .option('--check', 'Enable type checking and linting')
     .option(...configOption)
     .action(lazy(() => import('./app/serve').then(m => m.default)));
@@ -188,7 +188,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('backend:build')
-    .description('Build a backend plugin')
+    .description('Build a backend plugin [DEPRECATED]')
     .option('--minify', 'Minify the generated code')
     .option('--experimental-type-build', 'Enable experimental type build')
     .action(lazy(() => import('./backend/build').then(m => m.default)));
@@ -196,7 +196,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('backend:bundle')
-    .description('Bundle the backend into a deployment archive')
+    .description('Bundle the backend into a deployment archive [DEPRECATED]')
     .option(
       '--build-dependencies',
       'Build all local package dependencies before bundling the backend',
@@ -206,7 +206,9 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('backend:dev')
-    .description('Start local development server with HMR for the backend')
+    .description(
+      'Start local development server with HMR for the backend [DEPRECATED]',
+    )
     .option('--check', 'Enable type checking and linting')
     .option('--inspect', 'Enable debugger')
     .option('--inspect-brk', 'Enable debugger with await to attach debugger')
@@ -255,7 +257,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('plugin:build')
-    .description('Build a plugin')
+    .description('Build a plugin [DEPRECATED]')
     .option('--minify', 'Minify the generated code')
     .option('--experimental-type-build', 'Enable experimental type build')
     .action(lazy(() => import('./plugin/build').then(m => m.default)));
@@ -263,7 +265,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('plugin:serve')
-    .description('Serves the dev/ folder of a plugin')
+    .description('Serves the dev/ folder of a plugin [DEPRECATED]')
     .option('--check', 'Enable type checking and linting')
     .option(...configOption)
     .action(lazy(() => import('./plugin/serve').then(m => m.default)));
@@ -278,7 +280,7 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('build')
-    .description('Build a package for publishing')
+    .description('Build a package for publishing [DEPRECATED]')
     .option('--outputs <formats>', 'List of formats to output [types,cjs,esm]')
     .option('--minify', 'Minify the generated code')
     .option('--experimental-type-build', 'Enable experimental type build')
@@ -293,7 +295,7 @@ export function registerCommands(program: CommanderStatic) {
       'eslint-formatter-friendly',
     )
     .option('--fix', 'Attempt to automatically fix violations')
-    .description('Lint a package')
+    .description('Lint a package [DEPRECATED]')
     .action(lazy(() => import('./lint').then(m => m.default)));
 
   // TODO(Rugvip): Deprecate in favor of package variant
@@ -301,7 +303,9 @@ export function registerCommands(program: CommanderStatic) {
     .command('test')
     .allowUnknownOption(true) // Allows the command to run, but we still need to parse raw args
     .helpOption(', --backstage-cli-help') // Let Jest handle help
-    .description('Run tests, forwarding args to Jest, defaulting to watch mode')
+    .description(
+      'Run tests, forwarding args to Jest, defaulting to watch mode [DEPRECATED]',
+    )
     .action(lazy(() => import('./testCommand').then(m => m.default)));
 
   program
@@ -385,19 +389,23 @@ export function registerCommands(program: CommanderStatic) {
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('prepack')
-    .description('Prepares a package for packaging before publishing')
+    .description(
+      'Prepares a package for packaging before publishing [DEPRECATED]',
+    )
     .action(lazy(() => import('./pack').then(m => m.pre)));
 
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('postpack')
-    .description('Restores the changes made by the prepack command')
+    .description(
+      'Restores the changes made by the prepack command [DEPRECATED]',
+    )
     .action(lazy(() => import('./pack').then(m => m.post)));
 
   // TODO(Rugvip): Deprecate in favor of package variant
   program
     .command('clean')
-    .description('Delete cache directories')
+    .description('Delete cache directories [DEPRECATED]')
     .action(lazy(() => import('./clean/clean').then(m => m.default)));
 
   program