diff --git a/packages/create-plugin/src/constants.ts b/packages/create-plugin/src/constants.ts
index 42c416f78..d4bd1dd53 100644
--- a/packages/create-plugin/src/constants.ts
+++ b/packages/create-plugin/src/constants.ts
@@ -85,7 +85,7 @@ export const MIGRATION_CONFIG = {
 
 export const UDPATE_CONFIG = {
   // Files that should be overriden between configuration version updates.
-  filesToOverride: ['.config/'],
+  filesToOverride: ['.config/', '.cprc.json'],
 };
 
 // prettier-ignore
diff --git a/packages/create-plugin/src/utils/tests/utils.config.test.ts b/packages/create-plugin/src/utils/tests/utils.config.test.ts
index 01125a4ab..b7989169a 100644
--- a/packages/create-plugin/src/utils/tests/utils.config.test.ts
+++ b/packages/create-plugin/src/utils/tests/utils.config.test.ts
@@ -9,6 +9,7 @@ import { DEFAULT_FEATURE_FLAGS } from '../../constants.js';
 const mocks = vi.hoisted(() => {
   return {
     commandName: 'generate',
+    argv: {},
   };
 });
 
@@ -25,6 +26,7 @@ describe('getConfig', () => {
   describe('Command: Generate', () => {
     beforeEach(() => {
       mocks.commandName = 'generate';
+      mocks.argv = {};
     });
 
     it('should give back a default config', async () => {
@@ -35,11 +37,24 @@ describe('getConfig', () => {
         features: DEFAULT_FEATURE_FLAGS,
       });
     });
+
+    it('should override default feature flags via cli args', async () => {
+      mocks.argv = {
+        'feature-flags': 'bundleGrafanaUI',
+      };
+      const config = getConfig(tmpDir);
+
+      expect(config).toEqual({
+        version: getVersion(),
+        features: { ...DEFAULT_FEATURE_FLAGS, bundleGrafanaUI: true },
+      });
+    });
   });
 
   describe('Command: Update', () => {
     beforeEach(() => {
       mocks.commandName = 'update';
+      mocks.argv = {};
     });
 
     it('should give back the correct config when there are no config files at all', async () => {
diff --git a/packages/create-plugin/src/utils/tests/utils.helpers.test.ts b/packages/create-plugin/src/utils/tests/utils.helpers.test.ts
new file mode 100644
index 000000000..26fee5b6c
--- /dev/null
+++ b/packages/create-plugin/src/utils/tests/utils.helpers.test.ts
@@ -0,0 +1,58 @@
+import { partitionArr } from '../utils.helpers.js';
+
+describe('partitionArr', () => {
+  it('should partition an array of numbers based on a predicate', () => {
+    const arr = [1, 2, 3, 4, 5, 6];
+    const isEven = (num: number) => num % 2 === 0;
+    const result = partitionArr(arr, isEven);
+    expect(result).toEqual([
+      [2, 4, 6],
+      [1, 3, 5],
+    ]);
+  });
+
+  it('should partition an array of strings based on a predicate', () => {
+    const arr = ['apple', 'banana', 'cherry', 'date'];
+    const startsWithA = (str: string) => str[0] === 'a';
+    const result = partitionArr(arr, startsWithA);
+    expect(result).toEqual([['apple'], ['banana', 'cherry', 'date']]);
+  });
+
+  it('should return two empty arrays if the input array is empty', () => {
+    const arr: number[] = [];
+    const isEven = (num: number) => num % 2 === 0;
+    const result = partitionArr(arr, isEven);
+    expect(result).toEqual([[], []]);
+  });
+
+  it('should place all items in the first partition if all match the predicate', () => {
+    const arr = [2, 4, 6, 8];
+    const isEven = (num: number) => num % 2 === 0;
+    const result = partitionArr(arr, isEven);
+    expect(result).toEqual([[2, 4, 6, 8], []]);
+  });
+
+  it('should place all items in the second partition if none match the predicate', () => {
+    const arr = [1, 3, 5, 7];
+    const isEven = (num: number) => num % 2 === 0;
+    const result = partitionArr(arr, isEven);
+    expect(result).toEqual([[], [1, 3, 5, 7]]);
+  });
+
+  it('should work with a complex object array and predicate', () => {
+    const arr = [
+      { name: 'Alice', age: 25 },
+      { name: 'Bob', age: 30 },
+      { name: 'Charlie', age: 35 },
+    ];
+    const isUnder30 = (person: { name: string; age: number }) => person.age < 30;
+    const result = partitionArr(arr, isUnder30);
+    expect(result).toEqual([
+      [{ name: 'Alice', age: 25 }],
+      [
+        { name: 'Bob', age: 30 },
+        { name: 'Charlie', age: 35 },
+      ],
+    ]);
+  });
+});
diff --git a/packages/create-plugin/src/utils/utils.config.ts b/packages/create-plugin/src/utils/utils.config.ts
index ec08d2e9d..4954e103a 100644
--- a/packages/create-plugin/src/utils/utils.config.ts
+++ b/packages/create-plugin/src/utils/utils.config.ts
@@ -1,8 +1,10 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { getVersion } from './utils.version.js';
-import { commandName } from './utils.cli.js';
+import { argv, commandName } from './utils.cli.js';
 import { DEFAULT_FEATURE_FLAGS } from '../constants.js';
+import { printBox } from './utils.console.js';
+import { partitionArr } from './utils.helpers.js';
 
 export type FeatureFlags = {
   bundleGrafanaUI?: boolean;
@@ -21,6 +23,9 @@ export type UserConfig = {
   features: FeatureFlags;
 };
 
+// TODO: Create a config manager of sorts so we don't call getConfig multiple times rendering multiple warnings.
+let hasShownConfigWarnings = false;
+
 export function getConfig(workDir = process.cwd()): CreatePluginConfig {
   const rootConfig = getRootConfig(workDir);
   const userConfig = getUserConfig(workDir);
@@ -83,11 +88,32 @@ function readRCFileSync(path: string): CreatePluginConfig | undefined {
   }
 }
 
+// This function creates feature flags based on the defaults for generate command else flags read from config.
+// In all cases it will override the flags with the featureFlag cli arg values.
 function createFeatureFlags(flags?: FeatureFlags): FeatureFlags {
-  // Default values for new scaffoldings
-  if (commandName === 'generate') {
-    return DEFAULT_FEATURE_FLAGS;
+  const featureFlags = commandName === 'generate' ? DEFAULT_FEATURE_FLAGS : flags ?? {};
+  const cliArgFlags = parseFeatureFlagsFromCliArgs();
+  return { ...featureFlags, ...cliArgFlags };
+}
+
+function parseFeatureFlagsFromCliArgs() {
+  const flagsfromCliArgs: string[] = argv['feature-flags'] ? argv['feature-flags'].split(',') : [];
+  const availableFeatureFlags = Object.keys(DEFAULT_FEATURE_FLAGS);
+  const [knownFlags, unknownFlags] = partitionArr(flagsfromCliArgs, (item) => availableFeatureFlags.includes(item));
+
+  if (unknownFlags.length > 0 && !hasShownConfigWarnings) {
+    printBox({
+      title: 'Warning! Unknown feature flags detected.',
+      subtitle: ``,
+      content: `The following feature-flags are unknown: ${unknownFlags.join(
+        ', '
+      )}.\n\nAvailable feature-flags are: ${availableFeatureFlags.join(', ')}`,
+      color: 'yellow',
+    });
+    hasShownConfigWarnings = true;
   }
 
-  return flags ?? {};
+  return knownFlags.reduce((acc, flag) => {
+    return { ...acc, [flag]: true };
+  }, {} as FeatureFlags);
 }
diff --git a/packages/create-plugin/src/utils/utils.helpers.ts b/packages/create-plugin/src/utils/utils.helpers.ts
new file mode 100644
index 000000000..66a3af069
--- /dev/null
+++ b/packages/create-plugin/src/utils/utils.helpers.ts
@@ -0,0 +1,3 @@
+export function partitionArr<T>(arr: T[], pred: (item: T) => boolean): [T[], T[]] {
+  return arr.reduce<[T[], T[]]>((acc, i) => (acc[pred(i) ? 0 : 1].push(i), acc), [[], []]);
+}
diff --git a/packages/create-plugin/templates/common/.cprc.json b/packages/create-plugin/templates/common/.cprc.json
index 62fed26eb..bc6ba9919 100644
--- a/packages/create-plugin/templates/common/.cprc.json
+++ b/packages/create-plugin/templates/common/.cprc.json
@@ -1,8 +1,6 @@
 {
   "features": {
-    {{#if bundleGrafanaUI}}
-    "bundleGrafanaUI": true{{/if}}
-    {{#if useReactRouterV6}}
-    "useReactRouterV6": true{{/if}}
+    "bundleGrafanaUI": {{ bundleGrafanaUI }},
+    "useReactRouterV6": {{ useReactRouterV6 }}
   }
 }