diff --git a/.changeset/curvy-poets-dance.md b/.changeset/curvy-poets-dance.md
new file mode 100644
index 0000000000..abf478a729
--- /dev/null
+++ b/.changeset/curvy-poets-dance.md
@@ -0,0 +1,5 @@
+---
+'@backstage/cli': patch
+---
+
+Keep track of filtered configuration values when running frontend in development mode.
diff --git a/.changeset/large-flies-bow.md b/.changeset/large-flies-bow.md
new file mode 100644
index 0000000000..e571bc9a3c
--- /dev/null
+++ b/.changeset/large-flies-bow.md
@@ -0,0 +1,5 @@
+---
+'@backstage/config': patch
+---
+
+Add warning when trying to access configuration values that have been filtered out by visibility.
diff --git a/.changeset/sharp-seals-explode.md b/.changeset/sharp-seals-explode.md
new file mode 100644
index 0000000000..7dbcac7094
--- /dev/null
+++ b/.changeset/sharp-seals-explode.md
@@ -0,0 +1,5 @@
+---
+'@backstage/config-loader': patch
+---
+
+Add option to populate the `filteredKeys` property when processing configuration with a schema.
diff --git a/packages/cli/src/commands/app/serve.ts b/packages/cli/src/commands/app/serve.ts
index 85fbdd97a0..208042c719 100644
--- a/packages/cli/src/commands/app/serve.ts
+++ b/packages/cli/src/commands/app/serve.ts
@@ -59,6 +59,7 @@ export default async (cmd: Command) => {
     ...(await loadCliConfig({
       args: cmd.config,
       fromPackage: name,
+      withFilteredKeys: true,
     })),
   });
 
diff --git a/packages/cli/src/commands/plugin/serve.ts b/packages/cli/src/commands/plugin/serve.ts
index b9ba93bc62..a0200b7ce8 100644
--- a/packages/cli/src/commands/plugin/serve.ts
+++ b/packages/cli/src/commands/plugin/serve.ts
@@ -28,6 +28,7 @@ export default async (cmd: Command) => {
     ...(await loadCliConfig({
       args: cmd.config,
       fromPackage: name,
+      withFilteredKeys: true,
     })),
   });
 
diff --git a/packages/cli/src/lib/config.ts b/packages/cli/src/lib/config.ts
index db96ca7686..a93f040122 100644
--- a/packages/cli/src/lib/config.ts
+++ b/packages/cli/src/lib/config.ts
@@ -22,6 +22,7 @@ type Options = {
   args: string[];
   fromPackage?: string;
   mockEnv?: boolean;
+  withFilteredKeys?: boolean;
 };
 
 export async function loadCliConfig(options: Options) {
@@ -57,6 +58,7 @@ export async function loadCliConfig(options: Options) {
   try {
     const frontendAppConfigs = schema.process(appConfigs, {
       visibility: ['frontend'],
+      withFilteredKeys: options.withFilteredKeys,
     });
     const frontendConfig = ConfigReader.fromConfigs(frontendAppConfigs);
 
diff --git a/packages/config-loader/api-report.md b/packages/config-loader/api-report.md
index 37b9880448..47bc22c60f 100644
--- a/packages/config-loader/api-report.md
+++ b/packages/config-loader/api-report.md
@@ -59,7 +59,7 @@ export function readEnvConfig(env: {
 
 // Warnings were encountered during analysis:
 //
-// src/lib/schema/types.d.ts:77:5 - (ae-forgotten-export) The symbol "ConfigProcessingOptions" needs to be exported by the entry point index.d.ts
+// src/lib/schema/types.d.ts:83:5 - (ae-forgotten-export) The symbol "ConfigProcessingOptions" needs to be exported by the entry point index.d.ts
 // src/loader.d.ts:13:5 - (ae-forgotten-export) The symbol "EnvFunc" needs to be exported by the entry point index.d.ts
 
 // (No @packageDocumentation comment for this package)
diff --git a/packages/config-loader/src/lib/schema/filtering.test.ts b/packages/config-loader/src/lib/schema/filtering.test.ts
index 5079afa876..d4b3cd55b6 100644
--- a/packages/config-loader/src/lib/schema/filtering.test.ts
+++ b/packages/config-loader/src/lib/schema/filtering.test.ts
@@ -63,43 +63,115 @@ const visibility = new Map<string, ConfigVisibility>(
 
 describe('filterByVisibility', () => {
   test.each<[ConfigVisibility[], JsonObject]>([
-    [[], {}],
+    [
+      [],
+      {
+        data: {},
+        filteredKeys: [
+          'arr[0]',
+          'arr[1]',
+          'arr[2]',
+          'objArr[0].f',
+          'objArr[0].b',
+          'objArr[0].s',
+          'objArr[1].f',
+          'objArr[1].b',
+          'objArr[1].s',
+          'obj.f',
+          'obj.b.s',
+          'arrF[0].never',
+          'arrB[0].never',
+          'arrS[0].never',
+          'objF.never',
+          'objB.never',
+          'objS.never',
+        ],
+      },
+    ],
     [
       ['frontend'],
       {
-        arr: ['f'],
-        objArr: [{ f: 1 }, { f: 4 }],
-        obj: { f: 'a' },
-        arrF: [],
-        objF: {},
+        data: {
+          arr: ['f'],
+          objArr: [{ f: 1 }, { f: 4 }],
+          obj: { f: 'a' },
+          arrF: [],
+          objF: {},
+        },
+        filteredKeys: [
+          'arr[1]',
+          'arr[2]',
+          'objArr[0].b',
+          'objArr[0].s',
+          'objArr[1].b',
+          'objArr[1].s',
+          'obj.b.s',
+          'arrF[0].never',
+          'arrB[0].never',
+          'arrS[0].never',
+          'objF.never',
+          'objB.never',
+          'objS.never',
+        ],
       },
     ],
     [
       ['backend'],
       {
-        arr: ['b'],
-        objArr: [{ b: 2 }, { b: 5 }],
-        obj: { b: {} },
-        arrF: [{ never: 'here' }],
-        arrB: [{ never: 'here' }],
-        arrS: [{ never: 'here' }],
-        objF: { never: 'here' },
-        objB: { never: 'here' },
-        objS: { never: 'here' },
+        data: {
+          arr: ['b'],
+          objArr: [{ b: 2 }, { b: 5 }],
+          obj: { b: {} },
+          arrF: [{ never: 'here' }],
+          arrB: [{ never: 'here' }],
+          arrS: [{ never: 'here' }],
+          objF: { never: 'here' },
+          objB: { never: 'here' },
+          objS: { never: 'here' },
+        },
+        filteredKeys: [
+          'arr[0]',
+          'arr[2]',
+          'objArr[0].f',
+          'objArr[0].s',
+          'objArr[1].f',
+          'objArr[1].s',
+          'obj.f',
+          'obj.b.s',
+        ],
       },
     ],
     [
       ['secret'],
       {
-        arr: ['s'],
-        objArr: [{ s: 3 }, { s: 6 }],
-        obj: { b: { s: true } },
-        arrS: [],
-        objS: {},
+        data: {
+          arr: ['s'],
+          objArr: [{ s: 3 }, { s: 6 }],
+          obj: { b: { s: true } },
+          arrS: [],
+          objS: {},
+        },
+        filteredKeys: [
+          'arr[0]',
+          'arr[1]',
+          'objArr[0].f',
+          'objArr[0].b',
+          'objArr[1].f',
+          'objArr[1].b',
+          'obj.f',
+          'arrF[0].never',
+          'arrB[0].never',
+          'arrS[0].never',
+          'objF.never',
+          'objB.never',
+          'objS.never',
+        ],
       },
     ],
-    [['frontend', 'backend', 'secret'], data],
+    [['frontend', 'backend', 'secret'], { data, filteredKeys: [] }],
   ])('should filter correctly with %p', (filter, expected) => {
-    expect(filterByVisibility(data, filter, visibility)).toEqual(expected);
+    expect(
+      filterByVisibility(data, filter, visibility, undefined, true),
+    ).toEqual(expected);
   });
 });
diff --git a/packages/config-loader/src/lib/schema/filtering.ts b/packages/config-loader/src/lib/schema/filtering.ts
index 74d367a30a..3533be01b7 100644
--- a/packages/config-loader/src/lib/schema/filtering.ts
+++ b/packages/config-loader/src/lib/schema/filtering.ts
@@ -30,9 +30,17 @@ export function filterByVisibility(
   includeVisibilities: ConfigVisibility[],
   visibilityByPath: Map<string, ConfigVisibility>,
   transformFunc?: TransformFunc<number | string | boolean>,
-): JsonObject {
-  function transform(jsonVal: JsonValue, path: string): JsonValue | undefined {
-    const visibility = visibilityByPath.get(path) ?? DEFAULT_CONFIG_VISIBILITY;
+  withFilteredKeys?: boolean,
+): { data: JsonObject; filteredKeys?: string[] } {
+  const filteredKeys = new Array<string>();
+
+  function transform(
+    jsonVal: JsonValue,
+    visibilityPath: string, // Matches the format we get from ajv
+    filterPath: string, // Matches the format of the ConfigReader
+  ): JsonValue | undefined {
+    const visibility =
+      visibilityByPath.get(visibilityPath) ?? DEFAULT_CONFIG_VISIBILITY;
     const isVisible = includeVisibilities.includes(visibility);
 
     if (typeof jsonVal !== 'object') {
@@ -42,6 +50,9 @@ export function filterByVisibility(
         }
         return jsonVal;
       }
+      if (withFilteredKeys) {
+        filteredKeys.push(filterPath);
+      }
       return undefined;
     } else if (jsonVal === null) {
       return undefined;
@@ -49,7 +60,11 @@ export function filterByVisibility(
       const arr = new Array<JsonValue>();
 
       for (const [index, value] of jsonVal.entries()) {
-        const out = transform(value, `${path}/${index}`);
+        const out = transform(
+          value,
+          `${visibilityPath}/${index}`,
+          `${filterPath}[${index}]`,
+        );
         if (out !== undefined) {
           arr.push(out);
         }
@@ -68,7 +83,11 @@ export function filterByVisibility(
       if (value === undefined) {
         continue;
       }
-      const out = transform(value, `${path}/${key}`);
+      const out = transform(
+        value,
+        `${visibilityPath}/${key}`,
+        filterPath ? `${filterPath}.${key}` : key,
+      );
       if (out !== undefined) {
         outObj[key] = out;
         hasOutput = true;
@@ -81,5 +100,8 @@ export function filterByVisibility(
     return undefined;
   }
 
-  return (transform(data, '') as JsonObject) ?? {};
+  return {
+    filteredKeys: withFilteredKeys ? filteredKeys : undefined,
+    data: (transform(data, '', '') as JsonObject) ?? {},
+  };
 }
diff --git a/packages/config-loader/src/lib/schema/load.test.ts b/packages/config-loader/src/lib/schema/load.test.ts
index 4a2b719590..73fa55b90c 100644
--- a/packages/config-loader/src/lib/schema/load.test.ts
+++ b/packages/config-loader/src/lib/schema/load.test.ts
@@ -68,13 +68,19 @@ describe('loadConfigSchema', () => {
       schema.process(configs, {
         visibility: ['frontend'],
         valueTransform: () => 'X',
+        withFilteredKeys: true,
       }),
-    ).toEqual([{ data: { key1: 'X' }, context: 'test' }]);
+    ).toEqual([
+      { data: { key1: 'X' }, context: 'test', filteredKeys: ['key2'] },
+    ]);
     expect(
       schema.process(configs, {
         valueTransform: () => 'X',
+        withFilteredKeys: true,
       }),
-    ).toEqual([{ data: { key1: 'X', key2: 'X' }, context: 'test' }]);
+    ).toEqual([
+      { data: { key1: 'X', key2: 'X' }, context: 'test', filteredKeys: [] },
+    ]);
 
     const serialized = schema.serialize();
 
diff --git a/packages/config-loader/src/lib/schema/load.ts b/packages/config-loader/src/lib/schema/load.ts
index ae5823c8cc..b67bd0002f 100644
--- a/packages/config-loader/src/lib/schema/load.ts
+++ b/packages/config-loader/src/lib/schema/load.ts
@@ -57,7 +57,7 @@ export async function loadConfigSchema(
   return {
     process(
       configs: AppConfig[],
-      { visibility, valueTransform } = {},
+      { visibility, valueTransform, withFilteredKeys } = {},
     ): AppConfig[] {
       const result = validate(configs);
       if (result.errors) {
@@ -73,21 +73,23 @@ export async function loadConfigSchema(
       if (visibility) {
         processedConfigs = processedConfigs.map(({ data, context }) => ({
           context,
-          data: filterByVisibility(
+          ...filterByVisibility(
             data,
             visibility,
             result.visibilityByPath,
             valueTransform,
+            withFilteredKeys,
           ),
         }));
       } else if (valueTransform) {
         processedConfigs = processedConfigs.map(({ data, context }) => ({
           context,
-          data: filterByVisibility(
+          ...filterByVisibility(
             data,
             Array.from(CONFIG_VISIBILITIES),
             result.visibilityByPath,
             valueTransform,
+            withFilteredKeys,
           ),
         }));
       }
diff --git a/packages/config-loader/src/lib/schema/types.ts b/packages/config-loader/src/lib/schema/types.ts
index 30e47917bc..17090ad53c 100644
--- a/packages/config-loader/src/lib/schema/types.ts
+++ b/packages/config-loader/src/lib/schema/types.ts
@@ -96,6 +96,13 @@ type ConfigProcessingOptions = {
    * will be omitted.
    */
   valueTransform?: TransformFunc<any>;
+
+  /**
+   * Whether or not to include the `filteredKeys` property in the output `AppConfig`s.
+   *
+   * Default: `false`.
+   */
+  withFilteredKeys?: boolean;
 };
 
 /**
diff --git a/packages/config/api-report.md b/packages/config/api-report.md
index 50d2af0f1f..eff4236026 100644
--- a/packages/config/api-report.md
+++ b/packages/config/api-report.md
@@ -9,6 +9,7 @@
 export type AppConfig = {
   context: string;
   data: JsonObject;
+  filteredKeys?: string[];
 };
 
 // Warning: (ae-missing-release-tag) "Config" is exported by the package, but it is missing a release tag (@alpha, @beta, @public, or @internal)
diff --git a/packages/config/src/reader.test.ts b/packages/config/src/reader.test.ts
index b1ba536797..ed0ca7febe 100644
--- a/packages/config/src/reader.test.ts
+++ b/packages/config/src/reader.test.ts
@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+import { withLogCollector } from '../../test-utils-core/src';
 import { ConfigReader } from './reader';
 
 const DATA = {
@@ -185,6 +186,61 @@ describe('ConfigReader', () => {
     const config = new ConfigReader(DATA, CTX);
     expectInvalidValues(config);
   });
+
+  it('should warn when accessing filtered keys in development mode', () => {
+    const oldEnv = process.env.NODE_ENV;
+    (process.env as any).NODE_ENV = 'development';
+
+    const config = ConfigReader.fromConfigs([
+      {
+        data: DATA,
+        context: CTX,
+        filteredKeys: ['a', 'b[0]'],
+      },
+    ]);
+
+    expect(withLogCollector(() => config.getOptional('a'))).toMatchObject({
+      warn: [
+        "Failed to read configuration value at 'a' as it is not visible. See https://backstage.io/docs/conf/defining#visibility for instructions on how to make it visible.",
+      ],
+    });
+    expect(withLogCollector(() => config.getOptionalString('a'))).toMatchObject(
+      {
+        warn: [
+          "Failed to read configuration value at 'a' as it is not visible. See https://backstage.io/docs/conf/defining#visibility for instructions on how to make it visible.",
+        ],
+      },
+    );
+    expect(
+      withLogCollector(() => config.getOptionalConfigArray('b')),
+    ).toMatchObject({
+      warn: [
+        "Failed to read configuration array at 'b' as it does not have any visible elements. See https://backstage.io/docs/conf/defining#visibility for instructions on how to make it visible.",
+      ],
+    });
+
+    (process.env as any).NODE_ENV = oldEnv;
+  });
+
+  it('should not warn when accessing filtered keys outside of development mode', () => {
+    const config = ConfigReader.fromConfigs([
+      {
+        data: DATA,
+        context: CTX,
+        filteredKeys: ['a', 'b[0]'],
+      },
+    ]);
+
+    expect(withLogCollector(() => config.getOptional('a'))).toMatchObject({
+      warn: [],
+    });
+    expect(
+      withLogCollector(() => config.getOptionalString('a')),
+    ).toMatchObject({ warn: [] });
+    expect(
+      withLogCollector(() => config.getOptionalConfigArray('b')),
+    ).toMatchObject({ warn: [] });
+  });
 });
 
 describe('ConfigReader with fallback', () => {
diff --git a/packages/config/src/reader.ts b/packages/config/src/reader.ts
index 11346d4a50..d93706c12e 100644
--- a/packages/config/src/reader.ts
+++ b/packages/config/src/reader.ts
@@ -55,6 +55,15 @@ const errors = {
 };
 
 export class ConfigReader implements Config {
+  /**
+   * A set of key paths that where removed from the config due to not being visible.
+   *
+   * This was added as a mutable private member to avoid changes to the public API.
+   * Its only purpose of this is to warn users of missing visibility when running
+   * the frontend in development mode.
+   */
+  private filteredKeys?: string[];
+
   static fromConfigs(configs: AppConfig[]): ConfigReader {
     if (configs.length === 0) {
       return new ConfigReader(undefined);
@@ -62,9 +71,14 @@ export class ConfigReader implements Config {
 
     // Merge together all configs into a single config with recursive fallback
     // readers, giving the first config object in the array the lowest priority.
-    return configs.reduce<ConfigReader>((previousReader, { data, context }) => {
-      return new ConfigReader(data, context, previousReader);
-    }, undefined!);
+    return configs.reduce<ConfigReader>(
+      (previousReader, { data, context, filteredKeys }) => {
+        const reader = new ConfigReader(data, context, previousReader);
+        reader.filteredKeys = filteredKeys;
+        return reader;
+      },
+      undefined!,
+    );
   }
 
   constructor(
@@ -101,6 +115,18 @@ export class ConfigReader implements Config {
     const fallbackValue = this.fallback?.getOptional<T>(key);
 
     if (value === undefined) {
+      if (process.env.NODE_ENV === 'development') {
+        if (fallbackValue === undefined && key) {
+          const fullKey = this.fullKey(key);
+          if (this.filteredKeys?.includes(fullKey)) {
+            // eslint-disable-next-line no-console
+            console.warn(
+              `Failed to read configuration value at '${fullKey}' as it is not visible. ` +
+                'See https://backstage.io/docs/conf/defining#visibility for instructions on how to make it visible.',
+            );
+          }
+        }
+      }
       return fallbackValue;
     } else if (fallbackValue === undefined) {
       return value as T;
@@ -127,10 +153,9 @@ export class ConfigReader implements Config {
   getOptionalConfig(key: string): ConfigReader | undefined {
     const value = this.readValue(key);
     const fallbackConfig = this.fallback?.getOptionalConfig(key);
-    const prefix = this.fullKey(key);
 
     if (isObject(value)) {
-      return new ConfigReader(value, this.context, fallbackConfig, prefix);
+      return this.copy(value, key, fallbackConfig);
     }
     if (value !== undefined) {
       throw new TypeError(
@@ -163,18 +188,20 @@ export class ConfigReader implements Config {
     });
 
     if (!configs) {
+      if (process.env.NODE_ENV === 'development') {
+        const fullKey = this.fullKey(key);
+        if (this.filteredKeys?.some(k => k.startsWith(fullKey))) {
+          // eslint-disable-next-line no-console
+          console.warn(
+            `Failed to read configuration array at '${key}' as it does not have any visible elements. ` +
+              'See https://backstage.io/docs/conf/defining#visibility for instructions on how to make it visible.',
+          );
+        }
+      }
       return undefined;
     }
 
-    return configs.map(
-      (obj, index) =>
-        new ConfigReader(
-          obj,
-          this.context,
-          undefined,
-          this.fullKey(`${key}[${index}]`),
-        ),
-    );
+    return configs.map((obj, index) => this.copy(obj, `${key}[${index}]`));
   }
 
   getNumber(key: string): number {
@@ -261,6 +288,17 @@ export class ConfigReader implements Config {
     return `${this.prefix}${this.prefix ? '.' : ''}${key}`;
   }
 
+  private copy(data: JsonObject, key: string, fallback?: ConfigReader) {
+    const reader = new ConfigReader(
+      data,
+      this.context,
+      fallback,
+      this.fullKey(key),
+    );
+    reader.filteredKeys = this.filteredKeys;
+    return reader;
+  }
+
   private readConfigValue<T extends JsonValue>(
     key: string,
     validate: (
@@ -270,6 +308,17 @@ export class ConfigReader implements Config {
     const value = this.readValue(key);
 
     if (value === undefined) {
+      if (process.env.NODE_ENV === 'development') {
+        const fullKey = this.fullKey(key);
+        if (this.filteredKeys?.includes(fullKey)) {
+          // eslint-disable-next-line no-console
+          console.warn(
+            `Failed to read configuration value at '${fullKey}' as it is not visible. ` +
+              'See https://backstage.io/docs/conf/defining#visibility for instructions on how to make it visible.',
+          );
+        }
+      }
+
       return this.fallback?.readConfigValue(key, validate);
     }
     const result = validate(value);
diff --git a/packages/config/src/types.ts b/packages/config/src/types.ts
index d8f12f4f6e..1135e7d554 100644
--- a/packages/config/src/types.ts
+++ b/packages/config/src/types.ts
@@ -22,6 +22,7 @@ export type JsonValue = JsonObject | JsonArray | JsonPrimitive;
 export type AppConfig = {
   context: string;
   data: JsonObject;
+  filteredKeys?: string[];
 };
 
 export type Config = {