diff --git a/src/services/mcp/McpHub.ts b/src/services/mcp/McpHub.ts
index 1374e430fe..5d6c31a3e5 100644
--- a/src/services/mcp/McpHub.ts
+++ b/src/services/mcp/McpHub.ts
@@ -506,13 +506,23 @@ export class McpHub {
 		)
 		const fileExists = await fileExistsAtPath(mcpSettingsFilePath)
 		if (!fileExists) {
-			await fs.writeFile(
+			// Create the default settings file under the advisory lock. The merge
+			// callback preserves any config a concurrent process wrote between the
+			// existence check above and the locked read, instead of blindly
+			// truncating it (see #1371).
+			await safeWriteJson(
 				mcpSettingsFilePath,
-				`{
-  "mcpServers": {
-
-  }
-}`,
+				{ mcpServers: {} },
+				{
+					prettyPrint: true,
+					merge: (existing) => {
+						const parsed = existing as { mcpServers?: unknown } | null
+						if (parsed && parsed.mcpServers && typeof parsed.mcpServers === "object") {
+							return existing
+						}
+						return { mcpServers: {} }
+					},
+				},
 			)
 		}
 		return mcpSettingsFilePath
diff --git a/src/services/mcp/__tests__/McpHub.spec.ts b/src/services/mcp/__tests__/McpHub.spec.ts
index 96589d8dd6..cab1501b53 100644
--- a/src/services/mcp/__tests__/McpHub.spec.ts
+++ b/src/services/mcp/__tests__/McpHub.spec.ts
@@ -1,4 +1,5 @@
 import * as fs from "fs/promises"
+import * as path from "path"
 
 import type { Mock } from "vitest"
 import type { ExtensionContext, Uri } from "vscode"
@@ -34,12 +35,32 @@ import { safeWriteJson } from "../../../utils/safeWriteJson"
 
 // Mock safeWriteJson
 vi.mock("../../../utils/safeWriteJson", () => ({
-	safeWriteJson: vi.fn(async (filePath, data) => {
-		// Instead of trying to write to the file system, just call fs.writeFile mock
-		// This avoids the complex file locking and temp file operations
-		const fs = await import("fs/promises")
-		return fs.writeFile(filePath, JSON.stringify(data), "utf8")
-	}),
+	safeWriteJson: vi.fn(
+		async (
+			filePath: string,
+			data: unknown,
+			options?: { merge?: (existing: unknown, incoming: unknown) => unknown },
+		) => {
+			// Instead of trying to write to the file system, just call fs.writeFile mock
+			// This avoids the complex file locking and temp file operations.
+			// When a merge callback is provided, honor it: read the current on-disk
+			// content via the fs.readFile mock (simulating the read under the lock)
+			// and let the callback decide the final value.
+			let value = data
+			if (options?.merge) {
+				let existing: unknown = null
+				try {
+					const fs = await import("fs/promises")
+					existing = JSON.parse(await fs.readFile(filePath, "utf8"))
+				} catch {
+					existing = null
+				}
+				value = options.merge(existing, data)
+			}
+			const fs = await import("fs/promises")
+			return fs.writeFile(filePath, JSON.stringify(value), "utf8")
+		},
+	),
 }))
 
 vi.mock("delay", () => ({ default: vi.fn().mockResolvedValue(undefined) }))
@@ -212,6 +233,35 @@ describe("McpHub", () => {
 		watchSpy.mockRestore()
 	})
 
+	describe("getMcpSettingsFilePath", () => {
+		it("preserves a config written by a concurrent process during initial creation (#1371)", async () => {
+			const settingsPath = path.join("/mock/settings/path", "mcp_settings.json")
+			const concurrentConfig = {
+				mcpServers: {
+					"concurrent-server": { type: "stdio", command: "node", args: ["server.js"] },
+				},
+			}
+
+			// Window A's existence check sees the settings file as absent...
+			// (One-shot overrides: the factory defaults apply to all other tests.)
+			vi.mocked(fs.access).mockRejectedValueOnce(
+				Object.assign(new Error("ENOENT: no such file or directory"), { code: "ENOENT" }),
+			)
+			// ...but by the time the locked read runs (safeWriteJson merge),
+			// window B's config is already on disk.
+			vi.mocked(fs.readFile).mockResolvedValueOnce(JSON.stringify(concurrentConfig))
+
+			const returnedPath = await mcpHub.getMcpSettingsFilePath()
+
+			expect(returnedPath).toBe(settingsPath)
+			// The creation write must carry the concurrent config, not the empty stub.
+			expect(fs.writeFile).toHaveBeenCalledTimes(1)
+			const [writtenPath, writtenData] = vi.mocked(fs.writeFile).mock.calls[0]
+			expect(writtenPath).toBe(settingsPath)
+			expect(JSON.parse(writtenData as string)).toEqual(concurrentConfig)
+		})
+	})
+
 	describe("Discriminated union type handling", () => {
 		it("should create connected connections with proper type", async () => {
 			// Mock StdioClientTransport