diff --git a/.changeset/real-ants-perform.md b/.changeset/real-ants-perform.md
new file mode 100644
index 0000000000..8c06e78dc6
--- /dev/null
+++ b/.changeset/real-ants-perform.md
@@ -0,0 +1,5 @@
+---
+'@backstage/config': patch
+---
+
+Only warn once per key when trying to read visibility-filtered values
diff --git a/packages/config/src/reader.test.ts b/packages/config/src/reader.test.ts
index 2f846fe159..7f3513abf6 100644
--- a/packages/config/src/reader.test.ts
+++ b/packages/config/src/reader.test.ts
@@ -195,7 +195,7 @@ describe('ConfigReader', () => {
       {
         data: DATA,
         context: CTX,
-        filteredKeys: ['a', 'b[0]'],
+        filteredKeys: ['a', 'a2', 'b[0]'],
       },
     ]);
 
@@ -204,13 +204,13 @@ describe('ConfigReader', () => {
         "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.getOptionalString('a2')),
+    ).toMatchObject({
+      warn: [
+        "Failed to read configuration value at 'a2' 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({
@@ -222,6 +222,30 @@ describe('ConfigReader', () => {
     (process.env as any).NODE_ENV = oldEnv;
   });
 
+  it('only warns once 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'],
+      },
+    ]);
+
+    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.getOptional('a'))).toMatchObject({
+      warn: [],
+    });
+
+    (process.env as any).NODE_ENV = oldEnv;
+  });
+
   it('should not warn when accessing filtered keys outside of development mode', () => {
     const config = ConfigReader.fromConfigs([
       {
diff --git a/packages/config/src/reader.ts b/packages/config/src/reader.ts
index d93706c12e..c6f69e5b29 100644
--- a/packages/config/src/reader.ts
+++ b/packages/config/src/reader.ts
@@ -63,6 +63,7 @@ export class ConfigReader implements Config {
    * the frontend in development mode.
    */
   private filteredKeys?: string[];
+  private notifiedFilteredKeys = new Set<string>();
 
   static fromConfigs(configs: AppConfig[]): ConfigReader {
     if (configs.length === 0) {
@@ -118,7 +119,11 @@ export class ConfigReader implements Config {
       if (process.env.NODE_ENV === 'development') {
         if (fallbackValue === undefined && key) {
           const fullKey = this.fullKey(key);
-          if (this.filteredKeys?.includes(fullKey)) {
+          if (
+            this.filteredKeys?.includes(fullKey) &&
+            !this.notifiedFilteredKeys.has(fullKey)
+          ) {
+            this.notifiedFilteredKeys.add(fullKey);
             // eslint-disable-next-line no-console
             console.warn(
               `Failed to read configuration value at '${fullKey}' as it is not visible. ` +
@@ -190,7 +195,11 @@ export class ConfigReader implements Config {
     if (!configs) {
       if (process.env.NODE_ENV === 'development') {
         const fullKey = this.fullKey(key);
-        if (this.filteredKeys?.some(k => k.startsWith(fullKey))) {
+        if (
+          this.filteredKeys?.some(k => k.startsWith(fullKey)) &&
+          !this.notifiedFilteredKeys.has(key)
+        ) {
+          this.notifiedFilteredKeys.add(key);
           // eslint-disable-next-line no-console
           console.warn(
             `Failed to read configuration array at '${key}' as it does not have any visible elements. ` +
@@ -310,7 +319,11 @@ export class ConfigReader implements Config {
     if (value === undefined) {
       if (process.env.NODE_ENV === 'development') {
         const fullKey = this.fullKey(key);
-        if (this.filteredKeys?.includes(fullKey)) {
+        if (
+          this.filteredKeys?.includes(fullKey) &&
+          !this.notifiedFilteredKeys.has(fullKey)
+        ) {
+          this.notifiedFilteredKeys.add(fullKey);
           // eslint-disable-next-line no-console
           console.warn(
             `Failed to read configuration value at '${fullKey}' as it is not visible. ` +