diff --git a/packages/assets-controller/CHANGELOG.md b/packages/assets-controller/CHANGELOG.md
index 5c4942dea43..e8c3ed9ee8d 100644
--- a/packages/assets-controller/CHANGELOG.md
+++ b/packages/assets-controller/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - Preserve pooled-staking balances across Accounts API chain-slice updates (e.g. network switch / `replaceCoveredChainBalances`): exclude staking contract asset IDs from `AccountsApiDataSource` v5/v6 balance processing, and keep prior staked amounts when a merge replace omits them so Accounts API cannot reset staked ETH to missing/0 ([#9753](https://github.com/MetaMask/core/pull/9753))
+- Clean up unused `assetsInfo` and `assetsPrice` entries after a successful startup refresh so those persisted state slices no longer grow unbounded ([#9806](https://github.com/MetaMask/core/pull/9806))
 
 ## [13.1.1]
 
diff --git a/packages/assets-controller/src/AssetsController.test.ts b/packages/assets-controller/src/AssetsController.test.ts
index 075b220955f..a5f8fc8e635 100644
--- a/packages/assets-controller/src/AssetsController.test.ts
+++ b/packages/assets-controller/src/AssetsController.test.ts
@@ -2917,6 +2917,68 @@ describe('AssetsController', () => {
       });
     });
 
+    it('cleans up unused assetsInfo and assetsPrice entries after the startup refresh', async () => {
+      const unreferencedAssetId =
+        'eip155:1/erc20:0x6B175474E89094C44Da98b954EedeAC495271d0F' as Caip19AssetId;
+      const zeroBalanceAssetId =
+        'eip155:1/erc20:0xdAC17F958D2ee523a2206206994597C13D831ec7' as Caip19AssetId;
+      // Default tracked asset on a chain that is NOT enabled in this test
+      // (only eip155:1 is enabled): metadata is pre-seeded but no balance
+      // entry exists, and it must survive the cleanup.
+      const musdOnMonadAssetId =
+        'eip155:143/erc20:0xacA92E438df0B2401fF60dA7E4337B687a2435DA' as Caip19AssetId;
+
+      await withController(
+        {
+          clientControllerState: { isUiOpen: true },
+          state: {
+            assetsInfo: {
+              ...buildDefaultAssetsInfo(),
+              [unreferencedAssetId]: {
+                type: 'erc20',
+                symbol: 'DAI',
+                name: 'Dai Stablecoin',
+                decimals: 18,
+              },
+              [zeroBalanceAssetId]: {
+                type: 'erc20',
+                symbol: 'USDT',
+                name: 'Tether USD',
+                decimals: 6,
+              },
+            },
+            assetsPrice: {
+              [unreferencedAssetId]: {
+                assetPriceType: 'fungible',
+                price: 1,
+                usdPrice: 1,
+                lastUpdated: 0,
+              },
+            },
+            assetsBalance: {
+              [MOCK_ACCOUNT_ID]: { [zeroBalanceAssetId]: { amount: '0' } },
+            },
+          },
+        },
+        async ({ controller, messenger }) => {
+          expect(
+            controller.state.assetsInfo[unreferencedAssetId],
+          ).toBeDefined();
+
+          await activateTracking(messenger);
+
+          expect(
+            controller.state.assetsInfo[unreferencedAssetId],
+          ).toBeUndefined();
+          expect(
+            controller.state.assetsPrice[unreferencedAssetId],
+          ).toBeUndefined();
+          expect(controller.state.assetsInfo[zeroBalanceAssetId]).toBeDefined();
+          expect(controller.state.assetsInfo[musdOnMonadAssetId]).toBeDefined();
+        },
+      );
+    });
+
     it('stops tracking on keyring lock', async () => {
       await withController(async ({ messenger }) => {
         messenger.publish('KeyringController:unlock');
diff --git a/packages/assets-controller/src/AssetsController.ts b/packages/assets-controller/src/AssetsController.ts
index cee1e2daa56..d89f678e5b9 100644
--- a/packages/assets-controller/src/AssetsController.ts
+++ b/packages/assets-controller/src/AssetsController.ts
@@ -139,6 +139,7 @@ import type {
   SubscriptionResponse,
   Asset,
 } from './types.js';
+import { cleanupUnusedMetadata } from './utils/cleanupUnusedMetadata.js';
 import { ZERO_ADDRESS } from './utils/constants.js';
 import { pickRpcCustomAssetsSupplement } from './utils/customAssetsRpcSupplement.js';
 import {
@@ -1365,6 +1366,7 @@ export class AssetsController extends BaseController<
       this.#ensureDefaultTrackedAssetsSeeded();
       this.#subscribeAssets();
       this.#fetchMissingPricesWithoutCache(accounts, [...this.#enabledChains]);
+      this.update((state) => cleanupUnusedMetadata(state));
     } catch (error) {
       log('Failed to fetch assets on startup', error);
       this.#ensureNativeBalancesDefaultZero();
diff --git a/packages/assets-controller/src/utils/cleanupUnusedMetadata.test.ts b/packages/assets-controller/src/utils/cleanupUnusedMetadata.test.ts
new file mode 100644
index 00000000000..46185dfd264
--- /dev/null
+++ b/packages/assets-controller/src/utils/cleanupUnusedMetadata.test.ts
@@ -0,0 +1,262 @@
+import type { AssetsControllerState } from '../AssetsController.js';
+import type { AssetMetadata, AssetPrice, Caip19AssetId } from '../types.js';
+import { cleanupUnusedMetadata } from './cleanupUnusedMetadata.js';
+
+const SELECTED_ACCOUNT = 'account-1';
+const OTHER_ACCOUNT = 'account-2';
+
+/** USDC on mainnet (checksummed). */
+const HELD_ASSET = 'eip155:1/erc20:0xA0b86991c6218b36c1d19D4a2e9Eb0cE3606eB48';
+/** DAI on mainnet. */
+const UNREFERENCED_ASSET =
+  'eip155:1/erc20:0x6B175474E89094C44Da98b954EedeAC495271d0F';
+/** USDT on mainnet. */
+const ZERO_BALANCE_ASSET =
+  'eip155:1/erc20:0xdAC17F958D2ee523a2206206994597C13D831ec7';
+/** cbETH on Base. */
+const CUSTOM_ASSET =
+  'eip155:8453/erc20:0x2Ae3F1Ec7F1F5012CFEab0185bfc7aa3cf0DEc22';
+/** ETH on mainnet. */
+const NATIVE_SLIP44_ASSET = 'eip155:1/slip44:60';
+/** SOL — slip44 native on a chain outside the hardcoded (EVM-only) registry. */
+const NATIVE_SOLANA_ASSET =
+  'solana:5eykt4UsFv8P8NJdTREpY1vzqKqZKvdp/slip44:501';
+/** Zero-address ERC-20 native convention on a chain with no registry entry. */
+const NATIVE_ZERO_ADDRESS_ASSET =
+  'eip155:424242/erc20:0x0000000000000000000000000000000000000000';
+/** METIS — native only recognizable through the hardcoded registry. */
+const NATIVE_REGISTRY_ASSET =
+  'eip155:1088/erc20:0xdeaddeaddeaddeaddeaddeaddeaddeaddead0000';
+/** mUSD on Monad — default tracked, has metadata but no balance until the chain is enabled. */
+const MUSD_ON_MONAD_ASSET =
+  'eip155:143/erc20:0xacA92E438df0B2401fF60dA7E4337B687a2435DA';
+/** BAYC #1234 — NFT asset IDs carry a tokenId suffix. */
+const NFT_ASSET =
+  'eip155:1/erc721:0xBC4CA0EdA7647A8aB7C2061c2E118A18a936f13D/1234';
+
+function buildMetadata(symbol: string): AssetMetadata {
+  return { type: 'erc20', symbol, name: symbol, decimals: 18 };
+}
+
+function buildPrice(value: number): AssetPrice {
+  return {
+    assetPriceType: 'fungible',
+    price: value,
+    usdPrice: value,
+    lastUpdated: 1700000000000,
+  };
+}
+
+function buildState(
+  overrides: Partial<AssetsControllerState> = {},
+): AssetsControllerState {
+  return {
+    assetsInfo: {},
+    assetsBalance: {},
+    assetsPrice: {},
+    customAssets: {},
+    assetPreferences: {},
+    selectedCurrency: 'usd',
+    ...overrides,
+  };
+}
+
+type CleanupCase = {
+  description: string;
+  assetId: string;
+  /** State slices referencing the asset (none means unreferenced). */
+  references?: Partial<AssetsControllerState>;
+  expectKept: boolean;
+};
+
+const cleanupCases: CleanupCase[] = [
+  {
+    description: 'removes an asset that nothing references',
+    assetId: UNREFERENCED_ASSET,
+    expectKept: false,
+  },
+  {
+    description: 'removes a malformed asset ID that nothing references',
+    assetId: 'not-a-caip-id',
+    expectKept: false,
+  },
+  {
+    description: 'removes an unreferenced NFT asset ID',
+    assetId: NFT_ASSET,
+    expectKept: false,
+  },
+  {
+    description: 'keeps an asset with a non-zero balance',
+    assetId: HELD_ASSET,
+    references: {
+      assetsBalance: { [SELECTED_ACCOUNT]: { [HELD_ASSET]: { amount: '5' } } },
+    },
+    expectKept: true,
+  },
+  {
+    description: 'keeps an asset whose only balance entry is a zero amount',
+    assetId: ZERO_BALANCE_ASSET,
+    references: {
+      assetsBalance: {
+        [SELECTED_ACCOUNT]: { [ZERO_BALANCE_ASSET]: { amount: '0' } },
+      },
+    },
+    expectKept: true,
+  },
+  {
+    description: 'keeps an asset held only by a non-selected account',
+    assetId: HELD_ASSET,
+    references: {
+      assetsBalance: {
+        [SELECTED_ACCOUNT]: {},
+        [OTHER_ACCOUNT]: { [HELD_ASSET]: { amount: '42' } },
+      },
+    },
+    expectKept: true,
+  },
+  {
+    description: 'keeps an asset that is only referenced by customAssets',
+    assetId: CUSTOM_ASSET,
+    references: { customAssets: { [SELECTED_ACCOUNT]: [CUSTOM_ASSET] } },
+    expectKept: true,
+  },
+  {
+    description: 'keeps an asset whose balance key differs in casing',
+    assetId: HELD_ASSET,
+    references: {
+      assetsBalance: {
+        [SELECTED_ACCOUNT]: { [HELD_ASSET.toLowerCase()]: { amount: '1' } },
+      },
+    },
+    expectKept: true,
+  },
+  {
+    description: 'keeps an asset whose customAssets entry differs in casing',
+    assetId: CUSTOM_ASSET,
+    references: {
+      customAssets: {
+        [SELECTED_ACCOUNT]: [CUSTOM_ASSET.toLowerCase() as Caip19AssetId],
+      },
+    },
+    expectKept: true,
+  },
+  {
+    description: 'keeps a malformed asset ID that a balance entry references',
+    assetId: 'not-a-caip-id',
+    references: {
+      assetsBalance: {
+        [SELECTED_ACCOUNT]: { 'not-a-caip-id': { amount: '1' } },
+      },
+    },
+    expectKept: true,
+  },
+  {
+    description: 'keeps a slip44 native asset',
+    assetId: NATIVE_SLIP44_ASSET,
+    expectKept: true,
+  },
+  {
+    description: 'keeps a slip44 native on a chain outside the native registry',
+    assetId: NATIVE_SOLANA_ASSET,
+    expectKept: true,
+  },
+  {
+    description: 'keeps a zero-address ERC-20 native',
+    assetId: NATIVE_ZERO_ADDRESS_ASSET,
+    expectKept: true,
+  },
+  {
+    description: 'keeps a registry-only native (METIS dead address)',
+    assetId: NATIVE_REGISTRY_ASSET,
+    expectKept: true,
+  },
+  {
+    description:
+      'keeps a default tracked asset with no balance (mUSD on a disabled chain)',
+    assetId: MUSD_ON_MONAD_ASSET,
+    expectKept: true,
+  },
+];
+
+describe('cleanupUnusedMetadata', () => {
+  it.each(cleanupCases)(
+    '$description',
+    ({ assetId, references = {}, expectKept }) => {
+      const state = buildState({
+        assetsInfo: { [assetId]: buildMetadata('TEST') },
+        assetsPrice: { [assetId]: buildPrice(1) },
+        ...references,
+      });
+
+      cleanupUnusedMetadata(state);
+
+      expect(state.assetsInfo).toStrictEqual(
+        expectKept ? { [assetId]: buildMetadata('TEST') } : {},
+      );
+      expect(state.assetsPrice).toStrictEqual(
+        expectKept ? { [assetId]: buildPrice(1) } : {},
+      );
+    },
+  );
+
+  it('removes only unreferenced entries, leaving referenced ones in place', () => {
+    const state = buildState({
+      assetsInfo: {
+        [HELD_ASSET]: buildMetadata('USDC'),
+        [UNREFERENCED_ASSET]: buildMetadata('DAI'),
+      },
+      assetsPrice: {
+        [HELD_ASSET]: buildPrice(1),
+        [UNREFERENCED_ASSET]: buildPrice(1),
+      },
+      assetsBalance: {
+        [SELECTED_ACCOUNT]: { [HELD_ASSET]: { amount: '5000000' } },
+      },
+    });
+
+    cleanupUnusedMetadata(state);
+
+    expect(state.assetsInfo).toStrictEqual({
+      [HELD_ASSET]: buildMetadata('USDC'),
+    });
+    expect(state.assetsPrice).toStrictEqual({ [HELD_ASSET]: buildPrice(1) });
+  });
+
+  it('removes an unreferenced price entry even when the asset has no assetsInfo entry', () => {
+    const state = buildState({
+      assetsPrice: { [UNREFERENCED_ASSET]: buildPrice(1) },
+    });
+
+    cleanupUnusedMetadata(state);
+
+    expect(state.assetsPrice).toStrictEqual({});
+  });
+
+  it('leaves assetPreferences untouched, including entries for removed assets', () => {
+    const state = buildState({
+      assetsInfo: { [UNREFERENCED_ASSET]: buildMetadata('DAI') },
+      assetsPrice: { [UNREFERENCED_ASSET]: buildPrice(1) },
+      assetPreferences: {
+        [UNREFERENCED_ASSET]: { hidden: true },
+        [HELD_ASSET]: { hidden: false },
+      },
+    });
+
+    cleanupUnusedMetadata(state);
+
+    expect(state.assetsInfo).toStrictEqual({});
+    expect(state.assetsPrice).toStrictEqual({});
+    expect(state.assetPreferences).toStrictEqual({
+      [UNREFERENCED_ASSET]: { hidden: true },
+      [HELD_ASSET]: { hidden: false },
+    });
+  });
+
+  it('does nothing on empty state', () => {
+    const state = buildState();
+
+    cleanupUnusedMetadata(state);
+
+    expect(state).toStrictEqual(buildState());
+  });
+});
diff --git a/packages/assets-controller/src/utils/cleanupUnusedMetadata.ts b/packages/assets-controller/src/utils/cleanupUnusedMetadata.ts
new file mode 100644
index 00000000000..85fb2c9187e
--- /dev/null
+++ b/packages/assets-controller/src/utils/cleanupUnusedMetadata.ts
@@ -0,0 +1,42 @@
+import { DEFAULT_TRACKED_ASSETS_BY_CHAIN } from '../defaults.js';
+import type { AssetsControllerStateInternal } from '../types.js';
+import { isNativeAssetId } from './native-assets.js';
+
+type AssetIdKeyedRecord = Record<string, unknown>;
+
+export type CleanupUnusedMetadataState = {
+  assetsInfo: AssetIdKeyedRecord;
+  assetsBalance: Record<string, AssetIdKeyedRecord>;
+  assetsPrice: AssetIdKeyedRecord;
+  customAssets: AssetsControllerStateInternal['customAssets'];
+};
+
+/**
+ * Delete `assetsInfo` / `assetsPrice` entries for assets that are not held,
+ * custom, default tracked, or native.
+ *
+ * @param state - The controller state to clean up (mutated in place).
+ */
+export function cleanupUnusedMetadata(state: CleanupUnusedMetadataState): void {
+  const defaultTrackedAssetIds = [
+    ...DEFAULT_TRACKED_ASSETS_BY_CHAIN.values(),
+  ].flat();
+  const heldAssetIds = Object.values(state.assetsBalance).flatMap(
+    (accountBalances) => Object.keys(accountBalances),
+  );
+  const customAssetIds = Object.values(state.customAssets).flat();
+
+  const keptAssetIds = new Set(
+    [...defaultTrackedAssetIds, ...heldAssetIds, ...customAssetIds].map(
+      (assetId) => assetId.toLowerCase(),
+    ),
+  );
+  const isUnused = (assetId: string): boolean =>
+    !keptAssetIds.has(assetId.toLowerCase()) && !isNativeAssetId(assetId);
+
+  for (const slice of [state.assetsInfo, state.assetsPrice]) {
+    for (const assetId of Object.keys(slice).filter(isUnused)) {
+      delete slice[assetId];
+    }
+  }
+}
diff --git a/packages/assets-controller/src/utils/native-assets.test.ts b/packages/assets-controller/src/utils/native-assets.test.ts
index b82cedfdeb9..44eb3a8011d 100644
--- a/packages/assets-controller/src/utils/native-assets.test.ts
+++ b/packages/assets-controller/src/utils/native-assets.test.ts
@@ -4,6 +4,7 @@ import { fetchWithErrorHandling } from '@metamask/controller-utils';
 import {
   buildNativeAssetsFromConstant,
   buildNativeAssetsFromApi,
+  isNativeAssetId,
 } from './native-assets.js';
 import { normalizeAssetId } from './normalizeAssetId.js';
 
@@ -25,6 +26,54 @@ describe('buildNativeAssetsFromConstant', () => {
   });
 });
 
+describe('isNativeAssetId', () => {
+  it.each([
+    {
+      description: 'a slip44 native on a chain in the hardcoded registry',
+      assetId: 'eip155:1/slip44:60',
+      expected: true,
+    },
+    {
+      description: 'a slip44 native on a chain outside the hardcoded registry',
+      assetId: 'solana:5eykt4UsFv8P8NJdTREpY1vzqKqZKvdp/slip44:501',
+      expected: true,
+    },
+    {
+      description: 'a zero-address ERC-20 native on an unregistered chain',
+      assetId: 'eip155:424242/erc20:0x0000000000000000000000000000000000000000',
+      expected: true,
+    },
+    {
+      description: 'a registry-only native (METIS dead address)',
+      assetId: 'eip155:1088/erc20:0xdeaddeaddeaddeaddeaddeaddeaddeaddead0000',
+      expected: true,
+    },
+    {
+      description: 'a registry-only native in a different casing',
+      assetId: 'eip155:1088/erc20:0xDEADDEADDEADDEADDEADDEADDEADDEADDEAD0000',
+      expected: true,
+    },
+    {
+      description: 'a regular ERC-20 token',
+      assetId: 'eip155:1/erc20:0xA0b86991c6218b36c1d19D4a2e9Eb0cE3606eB48',
+      expected: false,
+    },
+    {
+      description: 'a malformed asset ID',
+      assetId: 'not-a-caip-id',
+      expected: false,
+    },
+    {
+      description: 'an NFT asset ID with a token ID',
+      assetId:
+        'eip155:1/erc721:0xBC4CA0EdA7647A8aB7C2061c2E118A18a936f13D/1234',
+      expected: false,
+    },
+  ])('returns $expected for $description', ({ assetId, expected }) => {
+    expect(isNativeAssetId(assetId)).toBe(expected);
+  });
+});
+
 describe('buildNativeAssetsFromApi', () => {
   beforeEach(() => {
     fetchWithErrorHandlingMock.mockReset();
diff --git a/packages/assets-controller/src/utils/native-assets.ts b/packages/assets-controller/src/utils/native-assets.ts
index 5cf251974aa..47347e78a4f 100644
--- a/packages/assets-controller/src/utils/native-assets.ts
+++ b/packages/assets-controller/src/utils/native-assets.ts
@@ -1,8 +1,9 @@
 import { SPOT_PRICES_SUPPORT_INFO } from '@metamask/assets-controllers';
 import { fetchWithErrorHandling } from '@metamask/controller-utils';
-import { parseCaipAssetType } from '@metamask/utils';
+import { isCaipAssetType, parseCaipAssetType } from '@metamask/utils';
 
 import type { Caip19AssetId, ChainId } from '../types.js';
+import { ZERO_ADDRESS } from './constants.js';
 import { normalizeAssetId } from './normalizeAssetId.js';
 
 const CHAINID_NETWORK_URL = 'https://chainid.network/chains.json';
@@ -29,6 +30,37 @@ export function buildNativeAssetsFromConstant(): Record<
   return nativeAssetsMap;
 }
 
+const KNOWN_NATIVE_ASSET_IDS: ReadonlySet<string> = new Set(
+  Object.values(buildNativeAssetsFromConstant()).map((assetId) =>
+    assetId.toLowerCase(),
+  ),
+);
+
+/**
+ * Whether a CAIP-19 asset ID represents a chain's native asset — via the
+ * `slip44` namespace, the zero-address ERC-20 convention, or the hardcoded
+ * native asset registry (non-standard natives like METIS/MNT).
+ *
+ * @param assetId - The asset ID to check (any casing); malformed IDs are
+ * reported as non-native.
+ * @returns True when the asset ID is a native asset.
+ */
+export function isNativeAssetId(assetId: string): boolean {
+  if (KNOWN_NATIVE_ASSET_IDS.has(assetId.toLowerCase())) {
+    return true;
+  }
+  if (!isCaipAssetType(assetId)) {
+    return false;
+  }
+
+  const { assetNamespace, assetReference } = parseCaipAssetType(assetId);
+  return (
+    assetNamespace === 'slip44' ||
+    (assetNamespace === 'erc20' &&
+      assetReference.toLowerCase() === ZERO_ADDRESS)
+  );
+}
+
 /**
  * Fetches chain data from chainid.network and merges it with the seed
  * native asset map built from {@link buildNativeAssetsFromConstant}.