diff --git a/.changeset/gorgeous-apples-reply.md b/.changeset/gorgeous-apples-reply.md
new file mode 100644
index 0000000000..c781617d22
--- /dev/null
+++ b/.changeset/gorgeous-apples-reply.md
@@ -0,0 +1,5 @@
+---
+'@backstage/config-loader': minor
+---
+
+Forward `null` values read from configuration files in configuration data, rather treating them as absence of config.
diff --git a/packages/config-loader/src/sources/transform/apply.test.ts b/packages/config-loader/src/sources/transform/apply.test.ts
index ea87734036..9f1dfbc672 100644
--- a/packages/config-loader/src/sources/transform/apply.test.ts
+++ b/packages/config-loader/src/sources/transform/apply.test.ts
@@ -17,7 +17,7 @@
 import { applyConfigTransforms } from './apply';
 
 describe('applyConfigTransforms', () => {
-  it('should apply not transforms to input', async () => {
+  it('should apply no transforms to input', async () => {
     const data = applyConfigTransforms(
       {
         app: {
@@ -35,7 +35,8 @@ describe('applyConfigTransforms', () => {
       app: {
         title: 'Test',
         x: 1,
-        y: [true],
+        y: [null, true],
+        z: null,
       },
     });
   });
@@ -77,7 +78,8 @@ describe('applyConfigTransforms', () => {
       app: {
         title: ['T', 'e', 's', 't'],
         x: 2,
-        y: [true],
+        y: [null, true],
+        z: null,
       },
     });
   });
diff --git a/packages/config-loader/src/sources/transform/apply.ts b/packages/config-loader/src/sources/transform/apply.ts
index d0d8650fe7..48d9c5a1e8 100644
--- a/packages/config-loader/src/sources/transform/apply.ts
+++ b/packages/config-loader/src/sources/transform/apply.ts
@@ -58,7 +58,7 @@ export async function applyConfigTransforms(
     if (typeof obj !== 'object') {
       return obj;
     } else if (obj === null) {
-      return undefined;
+      return null;
     } else if (Array.isArray(obj)) {
       const arr = new Array<JsonValue>();