diff --git a/.changeset/migrate-cli-commands-to-cleye.md b/.changeset/migrate-cli-commands-to-cleye.md
index 45f76fb6af..e6792423ee 100644
--- a/.changeset/migrate-cli-commands-to-cleye.md
+++ b/.changeset/migrate-cli-commands-to-cleye.md
@@ -2,4 +2,4 @@
 '@backstage/cli': patch
 ---
 
-Migrated remaining CLI command handlers from `commander` to `cleye` for argument parsing. CLI flags are now displayed in kebab-case in help output (e.g. `--success-cache` instead of `--successCache`), but both forms are accepted transparently — no changes needed in existing scripts or CI configurations.
+Migrated remaining CLI command handlers from `commander` to `cleye` for argument parsing. Several camelCase CLI flags have been deprecated in favor of their kebab-case equivalents (e.g. `--successCache` → `--success-cache`). The old camelCase forms still work but will now log a deprecation warning. Please update any scripts or CI configurations to use the kebab-case versions.
diff --git a/packages/cli/src/modules/lint/commands/repo/lint.ts b/packages/cli/src/modules/lint/commands/repo/lint.ts
index 513c76e0a5..174282ffcf 100644
--- a/packages/cli/src/modules/lint/commands/repo/lint.ts
+++ b/packages/cli/src/modules/lint/commands/repo/lint.ts
@@ -40,6 +40,19 @@ function depCount(pkg: BackstagePackageJson) {
 }
 
 export default async ({ args, info }: CommandContext) => {
+  for (const flag of [
+    'outputFile',
+    'successCache',
+    'successCacheDir',
+    'maxWarnings',
+  ]) {
+    if (args.some(a => a === `--${flag}` || a.startsWith(`--${flag}=`))) {
+      process.stderr.write(
+        `DEPRECATION WARNING: --${flag} is deprecated, use the kebab-case form instead\n`,
+      );
+    }
+  }
+
   const {
     flags: {
       fix,
diff --git a/packages/cli/src/modules/new/commands/new.ts b/packages/cli/src/modules/new/commands/new.ts
index a4899cf509..082d0ca028 100644
--- a/packages/cli/src/modules/new/commands/new.ts
+++ b/packages/cli/src/modules/new/commands/new.ts
@@ -19,6 +19,14 @@ import { createNewPackage } from '../lib/createNewPackage';
 import type { CommandContext } from '../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
+  for (const flag of ['skipInstall', 'npmRegistry', 'baseVersion']) {
+    if (args.some(a => a === `--${flag}` || a.startsWith(`--${flag}=`))) {
+      process.stderr.write(
+        `DEPRECATION WARNING: --${flag} is deprecated, use the kebab-case form instead\n`,
+      );
+    }
+  }
+
   const {
     flags: {
       select,
diff --git a/packages/cli/src/modules/test/commands/repo/test.ts b/packages/cli/src/modules/test/commands/repo/test.ts
index 743aa87c3d..c331caf994 100644
--- a/packages/cli/src/modules/test/commands/repo/test.ts
+++ b/packages/cli/src/modules/test/commands/repo/test.ts
@@ -134,6 +134,14 @@ export function createFlagFinder(args: string[]) {
 export default async ({ args, info }: CommandContext) => {
   const testGlobal = global as TestGlobal;
 
+  for (const flag of ['successCache', 'successCacheDir', 'jestHelp']) {
+    if (args.some(a => a === `--${flag}` || a.startsWith(`--${flag}=`))) {
+      process.stderr.write(
+        `DEPRECATION WARNING: --${flag} is deprecated, use the kebab-case form instead\n`,
+      );
+    }
+  }
+
   // Parse Backstage-specific flags; unknown flags and arguments are left in
   // args so they can be forwarded to Jest.
   const { flags: opts } = cli(