diff --git a/.changeset/orange-crews-explain.md b/.changeset/orange-crews-explain.md
new file mode 100644
index 0000000000..4b831392eb
--- /dev/null
+++ b/.changeset/orange-crews-explain.md
@@ -0,0 +1,5 @@
+---
+'@backstage/cli': minor
+---
+
+**BREAKING**: Removed the deprecated `app.<key>` template variables from the `index.html` templating. These should be replaced by using `config.getString("app.<key>")` instead.
diff --git a/.changeset/tame-lions-know.md b/.changeset/tame-lions-know.md
new file mode 100644
index 0000000000..7f304b22ef
--- /dev/null
+++ b/.changeset/tame-lions-know.md
@@ -0,0 +1,5 @@
+---
+'@backstage/core-app-api': minor
+---
+
+**BREAKING**: Removed the deprecated `GithubAuth.normalizeScopes` method.
diff --git a/packages/cli/src/lib/bundler/config.ts b/packages/cli/src/lib/bundler/config.ts
index fe64f23209..bfd05807ad 100644
--- a/packages/cli/src/lib/bundler/config.ts
+++ b/packages/cli/src/lib/bundler/config.ts
@@ -15,7 +15,6 @@
  */
 
 import fs from 'fs-extra';
-import chalk from 'chalk';
 import { resolve as resolvePath } from 'path';
 import ForkTsCheckerWebpackPlugin from 'fork-ts-checker-webpack-plugin';
 import HtmlWebpackPlugin from 'html-webpack-plugin';
@@ -118,43 +117,11 @@ export async function createConfig(
     }),
   );
 
-  const appParamDeprecationMsg = chalk.red(
-    'DEPRECATION WARNING: using `app.<key>` in the index.html template is deprecated, use `config.getString("app.<key>")` instead.',
-  );
   plugins.push(
     new HtmlWebpackPlugin({
       template: paths.targetHtml,
       templateParameters: {
         publicPath: validBaseUrl.pathname.replace(/\/$/, ''),
-        app: {
-          get title() {
-            console.warn(appParamDeprecationMsg);
-            return frontendConfig.getString('app.title');
-          },
-          get baseUrl() {
-            console.warn(appParamDeprecationMsg);
-            return validBaseUrl.href;
-          },
-          get googleAnalyticsTrackingId() {
-            console.warn(appParamDeprecationMsg);
-            return frontendConfig.getOptionalString(
-              'app.googleAnalyticsTrackingId',
-            );
-          },
-          get datadogRum() {
-            console.warn(appParamDeprecationMsg);
-            return {
-              env: frontendConfig.getOptionalString('app.datadogRum.env'),
-              clientToken: frontendConfig.getOptionalString(
-                'app.datadogRum.clientToken',
-              ),
-              applicationId: frontendConfig.getOptionalString(
-                'app.datadogRum.applicationId',
-              ),
-              site: frontendConfig.getOptionalString('app.datadogRum.site'),
-            };
-          },
-        },
         config: frontendConfig,
       },
     }),
diff --git a/packages/config-loader/src/lib/schema/collect.ts b/packages/config-loader/src/lib/schema/collect.ts
index a05796139b..3ff161cec4 100644
--- a/packages/config-loader/src/lib/schema/collect.ts
+++ b/packages/config-loader/src/lib/schema/collect.ts
@@ -182,7 +182,7 @@ function compileTsSchemas(paths: string[]) {
         program,
         // All schemas should export a `Config` symbol
         'Config',
-        // This enables usage of @visibility and @deprecated in doc comments
+        // This enables the use of these tags in TSDoc comments
         {
           required: true,
           validationKeywords: ['visibility', 'deprecated'],
diff --git a/packages/core-app-api/api-report.md b/packages/core-app-api/api-report.md
index c52b953465..116b33c598 100644
--- a/packages/core-app-api/api-report.md
+++ b/packages/core-app-api/api-report.md
@@ -376,8 +376,6 @@ export type FlatRoutesProps = {
 export class GithubAuth {
   // (undocumented)
   static create(options: OAuthApiCreateOptions): typeof githubAuthApiRef.T;
-  // @deprecated (undocumented)
-  static normalizeScope(scope?: string): Set<string>;
 }
 
 // @public
diff --git a/packages/core-app-api/src/apis/implementations/auth/github/GithubAuth.ts b/packages/core-app-api/src/apis/implementations/auth/github/GithubAuth.ts
index b0af4c7ade..7efe4e95c6 100644
--- a/packages/core-app-api/src/apis/implementations/auth/github/GithubAuth.ts
+++ b/packages/core-app-api/src/apis/implementations/auth/github/GithubAuth.ts
@@ -47,19 +47,4 @@ export default class GithubAuth {
       defaultScopes,
     });
   }
-
-  /**
-   * @deprecated This method is deprecated and will be removed in a future release.
-   */
-  static normalizeScope(scope?: string): Set<string> {
-    if (!scope) {
-      return new Set();
-    }
-
-    const scopeList = Array.isArray(scope)
-      ? scope
-      : scope.split(/[\s|,]/).filter(Boolean);
-
-    return new Set(scopeList);
-  }
 }