diff --git a/apps/api/src/federation/dto/capabilities.dto.spec.ts b/apps/api/src/federation/dto/capabilities.dto.spec.ts
new file mode 100644
index 0000000..ded956c
--- /dev/null
+++ b/apps/api/src/federation/dto/capabilities.dto.spec.ts
@@ -0,0 +1,80 @@
+/**
+ * Capabilities DTO Tests
+ *
+ * Tests for FederationCapabilities validation.
+ */
+
+import { describe, it, expect } from "vitest";
+import { validate } from "class-validator";
+import { plainToInstance } from "class-transformer";
+import { FederationCapabilitiesDto } from "./capabilities.dto";
+
+describe("FederationCapabilitiesDto", () => {
+  it("should accept valid capabilities", async () => {
+    const plain = {
+      supportsQuery: true,
+      supportsCommand: false,
+      supportsEvent: true,
+      supportsAgentSpawn: false,
+      protocolVersion: "1.0",
+    };
+
+    const dto = plainToInstance(FederationCapabilitiesDto, plain);
+    const errors = await validate(dto);
+
+    expect(errors).toHaveLength(0);
+  });
+
+  it("should accept minimal valid capabilities", async () => {
+    const plain = {};
+
+    const dto = plainToInstance(FederationCapabilitiesDto, plain);
+    const errors = await validate(dto);
+
+    expect(errors).toHaveLength(0);
+  });
+
+  it("should reject invalid boolean for supportsQuery", async () => {
+    const plain = {
+      supportsQuery: "yes", // Should be boolean
+    };
+
+    const dto = plainToInstance(FederationCapabilitiesDto, plain);
+    const errors = await validate(dto);
+
+    expect(errors.length).toBeGreaterThan(0);
+    expect(errors[0].property).toBe("supportsQuery");
+  });
+
+  it("should reject invalid type for protocolVersion", async () => {
+    const plain = {
+      protocolVersion: 1.0, // Should be string
+    };
+
+    const dto = plainToInstance(FederationCapabilitiesDto, plain);
+    const errors = await validate(dto);
+
+    expect(errors.length).toBeGreaterThan(0);
+    expect(errors[0].property).toBe("protocolVersion");
+  });
+
+  it("should accept only specified fields", async () => {
+    const plain = {
+      supportsQuery: true,
+      supportsCommand: true,
+      supportsEvent: false,
+      supportsAgentSpawn: true,
+      protocolVersion: "1.0",
+    };
+
+    const dto = plainToInstance(FederationCapabilitiesDto, plain);
+    const errors = await validate(dto);
+
+    expect(errors).toHaveLength(0);
+    expect(dto.supportsQuery).toBe(true);
+    expect(dto.supportsCommand).toBe(true);
+    expect(dto.supportsEvent).toBe(false);
+    expect(dto.supportsAgentSpawn).toBe(true);
+    expect(dto.protocolVersion).toBe("1.0");
+  });
+});
diff --git a/apps/api/src/federation/dto/capabilities.dto.ts b/apps/api/src/federation/dto/capabilities.dto.ts
new file mode 100644
index 0000000..da606b5
--- /dev/null
+++ b/apps/api/src/federation/dto/capabilities.dto.ts
@@ -0,0 +1,32 @@
+/**
+ * Capabilities DTO
+ *
+ * Data Transfer Object for federation capabilities validation.
+ */
+
+import { IsBoolean, IsOptional, IsString } from "class-validator";
+
+/**
+ * DTO for validating FederationCapabilities structure
+ */
+export class FederationCapabilitiesDto {
+  @IsOptional()
+  @IsBoolean()
+  supportsQuery?: boolean;
+
+  @IsOptional()
+  @IsBoolean()
+  supportsCommand?: boolean;
+
+  @IsOptional()
+  @IsBoolean()
+  supportsEvent?: boolean;
+
+  @IsOptional()
+  @IsBoolean()
+  supportsAgentSpawn?: boolean;
+
+  @IsOptional()
+  @IsString()
+  protocolVersion?: string;
+}
diff --git a/apps/api/src/federation/dto/connection.dto.ts b/apps/api/src/federation/dto/connection.dto.ts
index 3a15765..e65ac79 100644
--- a/apps/api/src/federation/dto/connection.dto.ts
+++ b/apps/api/src/federation/dto/connection.dto.ts
@@ -4,8 +4,10 @@
  * Data Transfer Objects for federation connection API.
  */
 
-import { IsString, IsUrl, IsOptional, IsObject, IsNumber } from "class-validator";
+import { IsString, IsUrl, IsOptional, IsObject, IsNumber, ValidateNested } from "class-validator";
+import { Type } from "class-transformer";
 import { Sanitize, SanitizeObject } from "../../common/decorators/sanitize.decorator";
+import { FederationCapabilitiesDto } from "./capabilities.dto";
 
 /**
  * DTO for initiating a connection
@@ -57,8 +59,9 @@ export class IncomingConnectionRequestDto {
   @IsString()
   publicKey!: string;
 
-  @IsObject()
-  capabilities!: Record<string, unknown>;
+  @ValidateNested()
+  @Type(() => FederationCapabilitiesDto)
+  capabilities!: FederationCapabilitiesDto;
 
   @IsNumber()
   timestamp!: number;
diff --git a/apps/api/src/federation/federation.controller.spec.ts b/apps/api/src/federation/federation.controller.spec.ts
index 48b682f..320cbc1 100644
--- a/apps/api/src/federation/federation.controller.spec.ts
+++ b/apps/api/src/federation/federation.controller.spec.ts
@@ -339,5 +339,30 @@ describe("FederationController", () => {
       });
       expect(connectionService.handleIncomingConnectionRequest).toHaveBeenCalled();
     });
+
+    it("should validate capabilities structure with valid data", async () => {
+      const dto = {
+        instanceId: "remote-instance-456",
+        instanceUrl: "https://remote.example.com",
+        publicKey: "PUBLIC_KEY",
+        capabilities: {
+          supportsQuery: true,
+          supportsCommand: false,
+          supportsEvent: true,
+          supportsAgentSpawn: false,
+          protocolVersion: "1.0",
+        },
+        timestamp: Date.now(),
+        signature: "valid-signature",
+      };
+      vi.spyOn(connectionService, "handleIncomingConnectionRequest").mockResolvedValue(
+        mockConnection
+      );
+
+      const result = await controller.handleIncomingConnection(dto);
+
+      expect(result.status).toBe("pending");
+      expect(connectionService.handleIncomingConnectionRequest).toHaveBeenCalled();
+    });
   });
 });