diff --git a/examples/field_formats_example/tsconfig.json b/examples/field_formats_example/tsconfig.json
index 66e9d7db028c75..a7651b649e5b3d 100644
--- a/examples/field_formats_example/tsconfig.json
+++ b/examples/field_formats_example/tsconfig.json
@@ -1,5 +1,5 @@
 {
-  "extends": "../../tsconfig.json",
+  "extends": "../../tsconfig.base.json",
   "compilerOptions": {
     "outDir": "./target",
     "skipLibCheck": true
diff --git a/examples/files_example/tsconfig.json b/examples/files_example/tsconfig.json
index 2ce0ddb8f7d66e..9329f941c10065 100644
--- a/examples/files_example/tsconfig.json
+++ b/examples/files_example/tsconfig.json
@@ -1,5 +1,5 @@
 {
-  "extends": "../../tsconfig.json",
+  "extends": "../../tsconfig.base.json",
   "compilerOptions": {
     "outDir": "./target/types"
   },
diff --git a/examples/hello_world/tsconfig.json b/examples/hello_world/tsconfig.json
index f0741719540484..6cfb28f7b33171 100644
--- a/examples/hello_world/tsconfig.json
+++ b/examples/hello_world/tsconfig.json
@@ -1,5 +1,5 @@
 {
-  "extends": "../../tsconfig.json",
+  "extends": "../../tsconfig.base.json",
   "compilerOptions": {
     "outDir": "./target/types"
   },
diff --git a/examples/partial_results_example/tsconfig.json b/examples/partial_results_example/tsconfig.json
index ba03cbc8361896..97d4c752cc3b56 100644
--- a/examples/partial_results_example/tsconfig.json
+++ b/examples/partial_results_example/tsconfig.json
@@ -1,5 +1,5 @@
 {
-  "extends": "../../tsconfig.json",
+  "extends": "../../tsconfig.base.json",
   "compilerOptions": {
     "outDir": "./target",
     "skipLibCheck": true
diff --git a/src/dev/typescript/project.ts b/src/dev/typescript/project.ts
index 32245e26c69ec1..c148cccfa73512 100644
--- a/src/dev/typescript/project.ts
+++ b/src/dev/typescript/project.ts
@@ -174,4 +174,8 @@ export class Project {
       ? [this.tsConfigPath, ...this.baseProject.getConfigPaths()]
       : [this.tsConfigPath];
   }
+
+  public getProjectsDeep(): Project[] {
+    return this.baseProject ? [this, ...this.baseProject.getProjectsDeep()] : [this];
+  }
 }
diff --git a/src/dev/typescript/run_check_ts_projects_cli.ts b/src/dev/typescript/run_check_ts_projects_cli.ts
index 9156c52a23d019..c4998e67919575 100644
--- a/src/dev/typescript/run_check_ts_projects_cli.ts
+++ b/src/dev/typescript/run_check_ts_projects_cli.ts
@@ -12,6 +12,7 @@ import { run } from '@kbn/dev-cli-runner';
 import { asyncMapWithLimit } from '@kbn/std';
 import { createFailError } from '@kbn/dev-cli-errors';
 import { getRepoFiles } from '@kbn/get-repo-files';
+import { REPO_ROOT } from '@kbn/utils';
 import globby from 'globby';
 
 import { File } from '../file';
@@ -37,6 +38,25 @@ export async function runCheckTsProjectsCli() {
       const stats = new Stats();
       let failed = false;
 
+      const everyProjectDeep = new Set(PROJECTS.flatMap((p) => p.getProjectsDeep()));
+      for (const proj of everyProjectDeep) {
+        const [, ...baseConfigRels] = proj.getConfigPaths().map((p) => Path.relative(REPO_ROOT, p));
+        const configRel = Path.relative(REPO_ROOT, proj.tsConfigPath);
+
+        if (baseConfigRels[0] === 'tsconfig.json') {
+          failed = true;
+          log.error(
+            `[${configRel}]: This tsconfig extends the root tsconfig.json file and shouldn't. The root tsconfig.json file is not a valid base config, you probably want to point to the tsconfig.base.json file.`
+          );
+        }
+        if (configRel !== 'tsconfig.base.json' && !baseConfigRels.includes('tsconfig.base.json')) {
+          failed = true;
+          log.error(
+            `[${configRel}]: This tsconfig does not extend the tsconfig.base.json file either directly or indirectly. The TS config setup for the repo expects every tsconfig file to extend this base config file.`
+          );
+        }
+      }
+
       const pathsAndProjects = await asyncMapWithLimit(PROJECTS, 5, async (proj) => {
         const paths = await globby(proj.getIncludePatterns(), {
           ignore: proj.getExcludePatterns(),