diff --git a/packages/coding-agent/src/mcp/config.ts b/packages/coding-agent/src/mcp/config.ts
index a23eee852..1189d7fe0 100644
--- a/packages/coding-agent/src/mcp/config.ts
+++ b/packages/coding-agent/src/mcp/config.ts
@@ -244,8 +244,10 @@ function getRequestedExaMcpTools(config: MCPServerConfig): string[] | null {
 		}
 		if (!config.type || config.type === "stdio") {
 			const stdioConfig = config as { args?: string[] };
-			for (const arg of stdioConfig.args ?? []) {
-				const match = arg.match(/(?:^|[\s?&])tools=([^&\s]+)/i) ?? arg.match(/--?tools[=\s]([^\s]+)/i);
+			const args = stdioConfig.args ?? [];
+			for (let i = 0; i < args.length; i++) {
+				if (/^--?tools$/i.test(args[i])) return args[i + 1];
+				const match = args[i].match(/(?:^|[\s?&])tools=([^&\s]+)/i) ?? args[i].match(/--?tools[=\s]([^\s]+)/i);
 				if (match) return match[1];
 			}
 		}
diff --git a/packages/coding-agent/test/mcp-exa-filter.test.ts b/packages/coding-agent/test/mcp-exa-filter.test.ts
index 4ea89a8c7..cb36019f9 100644
--- a/packages/coding-agent/test/mcp-exa-filter.test.ts
+++ b/packages/coding-agent/test/mcp-exa-filter.test.ts
@@ -63,4 +63,17 @@ describe("Exa MCP filtering", () => {
 
 		expect(Object.keys(result.configs)).toEqual(["exa"]);
 	});
+
+	test("keeps a stdio exa server with a separate tools argument", () => {
+		const configs: Record<string, MCPServerConfig> = {
+			exa: {
+				type: "stdio",
+				command: "npx",
+				args: ["-y", "exa-mcp-server", "--tools", "web_search_exa,web_fetch_exa"],
+			},
+		};
+		const result = filterExaMCPServers(configs, { exa: SOURCE });
+
+		expect(Object.keys(result.configs)).toEqual(["exa"]);
+	});
 });