diff --git a/controlplane/src/core/bufservices/feature-flag/getFeatureFlagsInLatestCompositionByFederatedGraph.ts b/controlplane/src/core/bufservices/feature-flag/getFeatureFlagsInLatestCompositionByFederatedGraph.ts
index 08f5885297..a100d75fa2 100644
--- a/controlplane/src/core/bufservices/feature-flag/getFeatureFlagsInLatestCompositionByFederatedGraph.ts
+++ b/controlplane/src/core/bufservices/feature-flag/getFeatureFlagsInLatestCompositionByFederatedGraph.ts
@@ -81,7 +81,9 @@ export function getFeatureFlagsInLatestCompositionByFederatedGraph(
             namespaceId: namespace.id,
             includeSubgraphs: false,
           });
-          if (flag) {
+          // A disabled feature flag is no longer served in the latest composition (its router config is
+          // removed without recomposing), so exclude it even though its schema version rows still exist.
+          if (flag && flag.isEnabled) {
             featureFlags.push(flag);
           }
         }
diff --git a/controlplane/src/core/repositories/FeatureFlagRepository.ts b/controlplane/src/core/repositories/FeatureFlagRepository.ts
index cc255b8145..0d64c93875 100644
--- a/controlplane/src/core/repositories/FeatureFlagRepository.ts
+++ b/controlplane/src/core/repositories/FeatureFlagRepository.ts
@@ -1307,13 +1307,21 @@ export class FeatureFlagRepository {
   }: {
     baseSchemaVersionId: string;
   }) {
+    // A feature flag can have multiple composed schema versions against the same base schema version
+    // (e.g. recomposing the feature flag recomposes it against the unchanged base, so rows accumulate).
+    // Deduplicate by feature flag, keeping the latest composed version, so callers get one entry per flag.
     const ffSchemaVersions = await this.db
-      .select({
+      .selectDistinctOn([federatedGraphsToFeatureFlagSchemaVersions.featureFlagId], {
         id: federatedGraphsToFeatureFlagSchemaVersions.composedSchemaVersionId,
         featureFlagId: federatedGraphsToFeatureFlagSchemaVersions.featureFlagId,
       })
       .from(federatedGraphsToFeatureFlagSchemaVersions)
+      .innerJoin(
+        schemaVersion,
+        eq(schemaVersion.id, federatedGraphsToFeatureFlagSchemaVersions.composedSchemaVersionId),
+      )
       .where(eq(federatedGraphsToFeatureFlagSchemaVersions.baseCompositionSchemaVersionId, baseSchemaVersionId))
+      .orderBy(federatedGraphsToFeatureFlagSchemaVersions.featureFlagId, desc(schemaVersion.createdAt))
       .execute();
 
     if (ffSchemaVersions.length === 0) {
diff --git a/controlplane/test/feature-flag/get-feature-flags-in-latest-composition-by-federated-graph.test.ts b/controlplane/test/feature-flag/get-feature-flags-in-latest-composition-by-federated-graph.test.ts
index 847d8590d4..fb925a7e73 100644
--- a/controlplane/test/feature-flag/get-feature-flags-in-latest-composition-by-federated-graph.test.ts
+++ b/controlplane/test/feature-flag/get-feature-flags-in-latest-composition-by-federated-graph.test.ts
@@ -1,6 +1,7 @@
 import fs from 'node:fs';
 import { join } from 'node:path';
 import { EnumStatusCode } from '@wundergraph/cosmo-connect/dist/common/common_pb';
+import { formatISO } from 'date-fns';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
 import { afterAllSetup, beforeAllSetup, genID, genUniqueLabel } from '../../src/core/test-util.js';
 import {
@@ -11,6 +12,7 @@ import {
   DEFAULT_ROUTER_URL,
   DEFAULT_SUBGRAPH_URL_ONE,
   SetupTest,
+  toggleFeatureFlag,
 } from '../test-util.js';
 
 let dbname = '';
@@ -66,6 +68,87 @@ describe('GetFeatureFlagsInLatestCompositionByFederatedGraph', () => {
     expect(resp.featureFlags.some((f) => f.name === flagName)).toBe(true);
   });
 
+  test('Should return each feature flag only once when it has multiple compositions against the same base', async (testContext) => {
+    const { client, server } = await SetupTest({ dbname, enabledFeatures: ['split-config-loading'] });
+    testContext.onTestFinished(() => server.close());
+
+    const labels = [genUniqueLabel()];
+    const federatedGraphName = genID('fedGraph');
+
+    await createAndPublishSubgraph(
+      client,
+      'users',
+      'default',
+      fs.readFileSync(join(process.cwd(), 'test/test-data/feature-flags/users.graphql')).toString(),
+      labels,
+      DEFAULT_SUBGRAPH_URL_ONE,
+    );
+
+    await createThenPublishFeatureSubgraph(
+      client,
+      'users-feature',
+      'users',
+      'default',
+      fs.readFileSync(join(process.cwd(), 'test/test-data/feature-flags/users-feature.graphql')).toString(),
+      labels,
+      'http://localhost:4101',
+    );
+
+    const federatedGraphLabels = labels.map(({ key, value }) => `${key}=${value}`);
+    await createFederatedGraph(client, federatedGraphName, 'default', federatedGraphLabels, DEFAULT_ROUTER_URL);
+
+    const flagName = genID('flag');
+    await createFeatureFlag(client, flagName, labels, ['users-feature'], 'default', true);
+
+    // recomposeFeatureFlag recomposes only the feature flag against the existing base composition (the base
+    // schema version is unchanged). Each call creates another feature flag composition for the same\
+    // (base composition, feature flag) pair, which is the source of the duplicates in the dropdown.
+    const recomposeResp1 = await client.recomposeFeatureFlag({ name: flagName, namespace: 'default' });
+    expect(recomposeResp1.response?.code).toBe(EnumStatusCode.OK);
+
+    const recomposeResp2 = await client.recomposeFeatureFlag({ name: flagName, namespace: 'default' });
+    expect(recomposeResp2.response?.code).toBe(EnumStatusCode.OK);
+
+    const resp = await client.getFeatureFlagsInLatestCompositionByFederatedGraph({
+      federatedGraphName,
+      namespace: 'default',
+    });
+
+    expect(resp.response?.code).toBe(EnumStatusCode.OK);
+    // Despite multiple accumulated composition rows, the flag must appear exactly once.
+    expect(resp.featureFlags).toStrictEqual(expect.arrayContaining([expect.objectContaining({ name: flagName })]));
+    expect(resp.featureFlags).toHaveLength(1);
+
+    // Create a second, enabled feature flag. It is composed into the latest composition, so it shows up too.
+    const secondFlagName = genID('flag');
+    await createFeatureFlag(client, secondFlagName, labels, ['users-feature'], 'default', true);
+
+    const withSecondFlag = await client.getFeatureFlagsInLatestCompositionByFederatedGraph({
+      federatedGraphName,
+      namespace: 'default',
+    });
+    expect(withSecondFlag.response?.code).toBe(EnumStatusCode.OK);
+    expect(withSecondFlag.featureFlags).toStrictEqual(
+      expect.arrayContaining([
+        expect.objectContaining({ name: flagName }),
+        expect.objectContaining({ name: secondFlagName }),
+      ]),
+    );
+    expect(withSecondFlag.featureFlags).toHaveLength(2);
+
+    await toggleFeatureFlag(client, secondFlagName, false, 'default');
+
+    const afterDisable = await client.getFeatureFlagsInLatestCompositionByFederatedGraph({
+      federatedGraphName,
+      namespace: 'default',
+    });
+    expect(afterDisable.response?.code).toBe(EnumStatusCode.OK);
+    expect(afterDisable.featureFlags).toHaveLength(1);
+    expect(afterDisable.featureFlags).toStrictEqual(
+      expect.arrayContaining([expect.objectContaining({ name: flagName })]),
+    );
+  });
+
   test('Should return empty list when no feature flags exist', async (testContext) => {
     const { client, server } = await SetupTest({ dbname });
     testContext.onTestFinished(() => server.close());