diff --git a/packages/api/src/agents/__tests__/initialize.test.ts b/packages/api/src/agents/__tests__/initialize.test.ts
index 6636c13af6..d7fa396024 100644
--- a/packages/api/src/agents/__tests__/initialize.test.ts
+++ b/packages/api/src/agents/__tests__/initialize.test.ts
@@ -33,7 +33,7 @@ jest.mock('@librechat/agents', () => ({
 }));
 
 import { Providers } from '@librechat/agents';
-import { EModelEndpoint } from 'librechat-data-provider';
+import { EModelEndpoint, Tools } from 'librechat-data-provider';
 import type { Agent } from 'librechat-data-provider';
 import type { ServerRequest, InitializeResultBase, EndpointTokenConfig } from '~/types';
 import type { InitializeAgentDbMethods } from '../initialize';
@@ -126,6 +126,13 @@ function createMocks(overrides?: {
   maxOutputTokens?: number;
   endpointTokenConfig?: EndpointTokenConfig;
   useRealTokenLookup?: boolean;
+  providerTools?: unknown[];
+  loadedToolDefinitions?: Array<{
+    name: string;
+    description?: string;
+    parameters?: object;
+  }>;
+  structuredTools?: unknown[];
 }) {
   const {
     provider = Providers.OPENAI,
@@ -136,6 +143,9 @@ function createMocks(overrides?: {
     maxOutputTokens = 4096,
     endpointTokenConfig,
     useRealTokenLookup = false,
+    providerTools,
+    loadedToolDefinitions = [],
+    structuredTools = [],
   } = overrides ?? {};
 
   const resolvedOverrideProvider = overrideProvider ?? provider;
@@ -158,6 +168,7 @@ function createMocks(overrides?: {
   const mockGetOptions = jest.fn().mockResolvedValue({
     llmConfig: { model, maxTokens: maxOutputTokens },
     endpointTokenConfig,
+    ...(providerTools !== undefined ? { tools: providerTools } : {}),
   } satisfies InitializeResultBase);
 
   mockGetProviderConfig.mockReturnValue({
@@ -181,12 +192,12 @@ function createMocks(overrides?: {
   mockOptionalChainWithEmptyCheck.mockImplementation(realUtils.optionalChainWithEmptyCheck);
 
   const loadTools = jest.fn().mockResolvedValue({
-    tools: [],
+    tools: structuredTools,
     toolContextMap: {},
     dynamicToolContextMap: {},
     userMCPAuthMap: undefined,
     toolRegistry: undefined,
-    toolDefinitions: [],
+    toolDefinitions: loadedToolDefinitions,
     hasDeferredTools: false,
   });
 
@@ -202,6 +213,27 @@ function createMocks(overrides?: {
   return { agent, req, res, loadTools, db };
 }
 
+function countNamedWebSearchTools(tools: unknown[] | undefined): number {
+  return (
+    tools?.filter((tool) => {
+      if (tool == null || typeof tool !== 'object') {
+        return false;
+      }
+      const { name } = tool as { name?: unknown };
+      return name === Tools.web_search;
+    }).length ?? 0
+  );
+}
+
+function countWebSearchDefinitions(
+  toolDefinitions: Array<{ name: string }> | undefined,
+): number {
+  return (
+    toolDefinitions?.filter((toolDefinition) => toolDefinition.name === Tools.web_search).length ??
+    0
+  );
+}
+
 describe('initializeAgent — custom provider token lookup', () => {
   const CUSTOM_PROVIDER = 'EduGPT';
 
@@ -276,6 +308,123 @@ describe('initializeAgent — custom provider token lookup', () => {
   });
 });
 
+describe('initializeAgent — Anthropic web_search precedence', () => {
+  const nativeWebSearchTool = {
+    type: 'web_search_20250305',
+    name: Tools.web_search,
+  };
+  const libreChatWebSearchDefinition = {
+    name: Tools.web_search,
+    description: 'Search the web',
+    parameters: { type: 'object', properties: {} },
+  };
+
+  beforeEach(() => {
+    jest.clearAllMocks();
+  });
+
+  it('keeps Anthropic native web_search when LibreChat search is not selected', async () => {
+    const { agent, req, res, loadTools, db } = createMocks({
+      provider: Providers.ANTHROPIC,
+      providerTools: [nativeWebSearchTool],
+    });
+
+    const result = await initializeAgent(
+      {
+        req,
+        res,
+        agent,
+        loadTools,
+        endpointOption: { endpoint: EModelEndpoint.agents },
+        allowedProviders: new Set([Providers.ANTHROPIC]),
+        isInitialAgent: true,
+      },
+      db,
+    );
+
+    expect(result.tools).toEqual([nativeWebSearchTool]);
+    expect(countNamedWebSearchTools(result.tools)).toBe(1);
+    expect(countWebSearchDefinitions(result.toolDefinitions)).toBe(0);
+  });
+
+  it('keeps LibreChat web_search definitions when native Anthropic search is not enabled', async () => {
+    const { agent, req, res, loadTools, db } = createMocks({
+      provider: Providers.ANTHROPIC,
+      loadedToolDefinitions: [libreChatWebSearchDefinition],
+    });
+    agent.tools = [Tools.web_search];
+
+    const result = await initializeAgent(
+      {
+        req,
+        res,
+        agent,
+        loadTools,
+        endpointOption: { endpoint: EModelEndpoint.agents },
+        allowedProviders: new Set([Providers.ANTHROPIC]),
+        isInitialAgent: true,
+      },
+      db,
+    );
+
+    expect(result.tools).toEqual([]);
+    expect(countNamedWebSearchTools(result.tools)).toBe(0);
+    expect(countWebSearchDefinitions(result.toolDefinitions)).toBe(1);
+  });
+
+  it('prefers LibreChat web_search when Anthropic native search is also enabled', async () => {
+    const { agent, req, res, loadTools, db } = createMocks({
+      provider: Providers.ANTHROPIC,
+      providerTools: [nativeWebSearchTool],
+      loadedToolDefinitions: [libreChatWebSearchDefinition],
+    });
+    agent.tools = [Tools.web_search];
+
+    const result = await initializeAgent(
+      {
+        req,
+        res,
+        agent,
+        loadTools,
+        endpointOption: { endpoint: EModelEndpoint.agents },
+        allowedProviders: new Set([Providers.ANTHROPIC]),
+        isInitialAgent: true,
+      },
+      db,
+    );
+
+    expect(result.tools).toEqual([]);
+    expect(countNamedWebSearchTools(result.tools)).toBe(0);
+    expect(countWebSearchDefinitions(result.toolDefinitions)).toBe(1);
+  });
+
+  it('leaves non-Anthropic providers unchanged', async () => {
+    const { agent, req, res, loadTools, db } = createMocks({
+      provider: Providers.OPENAI,
+      providerTools: [nativeWebSearchTool],
+      loadedToolDefinitions: [libreChatWebSearchDefinition],
+    });
+    agent.tools = [Tools.web_search];
+
+    const result = await initializeAgent(
+      {
+        req,
+        res,
+        agent,
+        loadTools,
+        endpointOption: { endpoint: EModelEndpoint.agents },
+        allowedProviders: new Set([Providers.OPENAI]),
+        isInitialAgent: true,
+      },
+      db,
+    );
+
+    expect(result.tools).toEqual([nativeWebSearchTool]);
+    expect(countNamedWebSearchTools(result.tools)).toBe(1);
+    expect(countWebSearchDefinitions(result.toolDefinitions)).toBe(1);
+  });
+});
+
 describe('initializeAgent — stable and dynamic instruction fields', () => {
   beforeEach(() => {
     jest.clearAllMocks();
diff --git a/packages/api/src/agents/initialize.ts b/packages/api/src/agents/initialize.ts
index b4985d356e..1b668a9eb0 100644
--- a/packages/api/src/agents/initialize.ts
+++ b/packages/api/src/agents/initialize.ts
@@ -65,6 +65,53 @@ function appendAdditionalInstructions(agent: Agent, text?: string | null): void
     .join('\n\n');
 }
 
+function getToolName(tool: unknown): string | undefined {
+  if (tool == null || typeof tool !== 'object') {
+    return undefined;
+  }
+  const { name } = tool as { name?: unknown };
+  return typeof name === 'string' ? name : undefined;
+}
+
+function hasToolDefinition(toolDefinitions: LCTool[] | undefined, name: string): boolean {
+  return toolDefinitions?.some((toolDefinition) => toolDefinition.name === name) === true;
+}
+
+function resolveAnthropicToolConflicts({
+  provider,
+  tools,
+  toolDefinitions,
+}: {
+  provider?: string;
+  tools?: unknown[];
+  toolDefinitions?: LCTool[];
+}): unknown[] | undefined {
+  if (provider !== Providers.ANTHROPIC || !tools?.length) {
+    return tools;
+  }
+
+  if (!hasToolDefinition(toolDefinitions, Tools.web_search)) {
+    return tools;
+  }
+
+  let removed = 0;
+  const resolvedTools = tools.filter((tool) => {
+    const shouldRemove = getToolName(tool) === Tools.web_search;
+    if (shouldRemove) {
+      removed += 1;
+    }
+    return !shouldRemove;
+  });
+
+  if (removed > 0) {
+    logger.debug(
+      `[initializeAgent] Removed ${removed} Anthropic native web_search tool(s); LibreChat web_search is enabled.`,
+    );
+  }
+
+  return resolvedTools;
+}
+
 /**
  * Extended agent type with additional fields needed after initialization
  */
@@ -825,14 +872,20 @@ export async function initializeAgent(
 
   /** Check for tool presence from either full instances or definitions (event-driven mode) */
   const hasAgentTools = (structuredTools?.length ?? 0) > 0 || (toolDefinitions?.length ?? 0) > 0;
+  const providerTools = resolveAnthropicToolConflicts({
+    provider: agent.provider,
+    tools: options.tools,
+    toolDefinitions,
+  });
+  const hasProviderTools = (providerTools?.length ?? 0) > 0;
 
-  let tools: GenericTool[] = options.tools?.length
-    ? (options.tools as GenericTool[])
+  let tools: GenericTool[] = hasProviderTools
+    ? (providerTools as GenericTool[])
     : (structuredTools ?? []);
 
   if (
     (agent.provider === Providers.GOOGLE || agent.provider === Providers.VERTEXAI) &&
-    options.tools?.length &&
+    hasProviderTools &&
     hasAgentTools
   ) {
     throw new Error(`{ "type": "${ErrorTypes.GOOGLE_TOOL_CONFLICT}"}`);
@@ -840,10 +893,10 @@ export async function initializeAgent(
     (agent.provider === Providers.OPENAI ||
       agent.provider === Providers.AZURE ||
       agent.provider === Providers.ANTHROPIC) &&
-    options.tools?.length &&
+    hasProviderTools &&
     structuredTools?.length
   ) {
-    tools = structuredTools.concat(options.tools as GenericTool[]);
+    tools = structuredTools.concat(providerTools as GenericTool[]);
   }
 
   agent.model_parameters = { ...options.llmConfig } as Agent['model_parameters'];