diff --git a/src/core/assistant-message/presentAssistantMessage.ts b/src/core/assistant-message/presentAssistantMessage.ts
index ada841c10d..6618439bc6 100644
--- a/src/core/assistant-message/presentAssistantMessage.ts
+++ b/src/core/assistant-message/presentAssistantMessage.ts
@@ -738,6 +738,7 @@ export async function presentAssistantMessage(cline: Task) {
 						block.params,
 						stateExperiments,
 						includedTools,
+						block.nativeArgs,
 					)
 				} catch (error) {
 					cline.consecutiveMistakeCount++
diff --git a/src/core/tools/validateToolUse.ts b/src/core/tools/validateToolUse.ts
index d057033741..4a784da790 100644
--- a/src/core/tools/validateToolUse.ts
+++ b/src/core/tools/validateToolUse.ts
@@ -32,6 +32,7 @@ export function validateToolUse(
 	toolParams?: Record<string, unknown>,
 	experiments?: Record<string, boolean>,
 	includedTools?: string[],
+	nativeArgs?: Record<string, unknown>,
 ): void {
 	// First, check if the tool name is actually a valid/known tool
 	// This catches completely invalid tool names like "edit_file" that don't exist
@@ -51,6 +52,7 @@ export function validateToolUse(
 			toolParams,
 			experiments,
 			includedTools,
+			nativeArgs,
 		)
 	) {
 		throw new Error(`Tool "${toolName}" is not allowed in ${mode} mode.`)
@@ -81,6 +83,7 @@ export function isToolAllowedForMode(
 	toolParams?: Record<string, any>, // All tool parameters
 	experiments?: Record<string, boolean>,
 	includedTools?: string[], // Opt-in tools explicitly included (e.g., from modelInfo)
+	nativeArgs?: Record<string, any>, // Native protocol arguments (e.g., nativeArgs.files for multi-file apply_diff)
 ): boolean {
 	// Always allow these tools
 	if (ALWAYS_AVAILABLE_TOOLS.includes(tool as any)) {
@@ -188,6 +191,37 @@ export function isToolAllowedForMode(
 					console.warn(`Failed to parse XML args for file restriction validation: ${error}`)
 				}
 			}
+
+			// Handle native protocol multi-file format (nativeArgs.files from multi_apply_diff schema)
+			if (nativeArgs?.files && Array.isArray(nativeArgs.files)) {
+				for (const file of nativeArgs.files) {
+					const filePath = file?.path
+					if (filePath && typeof filePath === "string") {
+						if (!doesFileMatchRegex(filePath, options.fileRegex)) {
+							throw new FileRestrictionError(
+								mode.name,
+								options.fileRegex,
+								options.description,
+								filePath,
+								tool,
+							)
+						}
+					}
+				}
+			}
+
+			// Handle native protocol single-file format (nativeArgs.path from apply_diff schema)
+			if (nativeArgs?.path && typeof nativeArgs.path === "string" && nativeArgs?.diff) {
+				if (!doesFileMatchRegex(nativeArgs.path, options.fileRegex)) {
+					throw new FileRestrictionError(
+						mode.name,
+						options.fileRegex,
+						options.description,
+						nativeArgs.path,
+						tool,
+					)
+				}
+			}
 		}
 
 		return true
diff --git a/src/shared/__tests__/modes.spec.ts b/src/shared/__tests__/modes.spec.ts
index a00abde787..db42cc2b57 100644
--- a/src/shared/__tests__/modes.spec.ts
+++ b/src/shared/__tests__/modes.spec.ts
@@ -300,6 +300,191 @@ describe("isToolAllowedForMode", () => {
 				}),
 			).toThrow(/Markdown files only/)
 		})
+
+		it("applies restrictions to apply_diff with native protocol multi-file format (nativeArgs.files)", () => {
+			// Test apply_diff with nativeArgs.files (native protocol multi-file format)
+			// This simulates the multi_apply_diff schema used with native protocol
+
+			// Should allow markdown files in architect mode
+			expect(
+				isToolAllowedForMode(
+					"apply_diff",
+					"architect",
+					[],
+					undefined,
+					{}, // toolParams is empty for native protocol
+					undefined,
+					undefined,
+					{ files: [{ path: "test.md", diff: "- old\n+ new" }] },
+				),
+			).toBe(true)
+
+			// Test with non-markdown file - should throw error
+			expect(() =>
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					files: [{ path: "test.py", diff: "- old\n+ new" }],
+				}),
+			).toThrow(FileRestrictionError)
+			expect(() =>
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					files: [{ path: "test.py", diff: "- old\n+ new" }],
+				}),
+			).toThrow(/Markdown files only/)
+
+			// Test with multiple markdown files - should allow
+			expect(
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					files: [
+						{ path: "readme.md", diff: "- old\n+ new" },
+						{ path: "docs.md", diff: "- old\n+ new" },
+					],
+				}),
+			).toBe(true)
+
+			// Test with mixed file types - should throw error for non-markdown
+			expect(() =>
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					files: [
+						{ path: "readme.md", diff: "- old\n+ new" },
+						{ path: "script.py", diff: "- old\n+ new" },
+					],
+				}),
+			).toThrow(FileRestrictionError)
+			expect(() =>
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					files: [
+						{ path: "readme.md", diff: "- old\n+ new" },
+						{ path: "script.py", diff: "- old\n+ new" },
+					],
+				}),
+			).toThrow(/Markdown files only/)
+		})
+
+		it("applies restrictions to apply_diff with native protocol single-file format (nativeArgs.path)", () => {
+			// Test apply_diff with nativeArgs.path (native protocol single-file format)
+			// This simulates the apply_diff schema used with native protocol
+
+			// Should allow markdown files in architect mode
+			expect(
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					path: "test.md",
+					diff: "- old\n+ new",
+				}),
+			).toBe(true)
+
+			// Test with non-markdown file - should throw error
+			expect(() =>
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					path: "test.py",
+					diff: "- old\n+ new",
+				}),
+			).toThrow(FileRestrictionError)
+			expect(() =>
+				isToolAllowedForMode("apply_diff", "architect", [], undefined, {}, undefined, undefined, {
+					path: "test.py",
+					diff: "- old\n+ new",
+				}),
+			).toThrow(/Markdown files only/)
+		})
+
+		it("applies native protocol file restrictions to custom modes with fileRegex", () => {
+			// Test that custom mode file restrictions work with native protocol formats
+			const customModesWithRegex: ModeConfig[] = [
+				{
+					slug: "ts-editor",
+					name: "TypeScript Editor",
+					roleDefinition: "You are a TypeScript editor",
+					groups: [
+						"read",
+						["edit", { fileRegex: "\\.tsx?$", description: "TypeScript files only" }],
+						"browser",
+					],
+				},
+			]
+
+			// Test native multi-file format with valid TS files
+			expect(
+				isToolAllowedForMode(
+					"apply_diff",
+					"ts-editor",
+					customModesWithRegex,
+					undefined,
+					{},
+					undefined,
+					undefined,
+					{
+						files: [
+							{ path: "app.ts", diff: "- old\n+ new" },
+							{ path: "component.tsx", diff: "- old\n+ new" },
+						],
+					},
+				),
+			).toBe(true)
+
+			// Test native multi-file format with invalid file
+			expect(() =>
+				isToolAllowedForMode(
+					"apply_diff",
+					"ts-editor",
+					customModesWithRegex,
+					undefined,
+					{},
+					undefined,
+					undefined,
+					{
+						files: [
+							{ path: "app.ts", diff: "- old\n+ new" },
+							{ path: "styles.css", diff: "- old\n+ new" },
+						],
+					},
+				),
+			).toThrow(FileRestrictionError)
+			expect(() =>
+				isToolAllowedForMode(
+					"apply_diff",
+					"ts-editor",
+					customModesWithRegex,
+					undefined,
+					{},
+					undefined,
+					undefined,
+					{
+						files: [
+							{ path: "app.ts", diff: "- old\n+ new" },
+							{ path: "styles.css", diff: "- old\n+ new" },
+						],
+					},
+				),
+			).toThrow(/TypeScript files only/)
+
+			// Test native single-file format with valid TS file
+			expect(
+				isToolAllowedForMode(
+					"apply_diff",
+					"ts-editor",
+					customModesWithRegex,
+					undefined,
+					{},
+					undefined,
+					undefined,
+					{ path: "app.ts", diff: "- old\n+ new" },
+				),
+			).toBe(true)
+
+			// Test native single-file format with invalid file
+			expect(() =>
+				isToolAllowedForMode(
+					"apply_diff",
+					"ts-editor",
+					customModesWithRegex,
+					undefined,
+					{},
+					undefined,
+					undefined,
+					{ path: "styles.css", diff: "- old\n+ new" },
+				),
+			).toThrow(FileRestrictionError)
+		})
 	})
 
 	it("handles non-existent modes", () => {