diff --git a/packages/coding-agent/src/core/sdk.ts b/packages/coding-agent/src/core/sdk.ts
index 93bb9ea5..985f7807 100644
--- a/packages/coding-agent/src/core/sdk.ts
+++ b/packages/coding-agent/src/core/sdk.ts
@@ -641,6 +641,13 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		sessionManager.appendThinkingLevelChange(thinkingLevel);
 	}
 
+	// Determine skillsSettings: if options.skills was explicitly provided (even []),
+	// mark skills as disabled so UI doesn't re-discover them
+	const skillsSettings =
+		options.skills !== undefined
+			? { ...settingsManager.getSkillsSettings(), enabled: false }
+			: settingsManager.getSkillsSettings();
+
 	const session = new AgentSession({
 		agent,
 		sessionManager,
@@ -648,7 +655,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		scopedModels: options.scopedModels,
 		promptTemplates: promptTemplates,
 		extensionRunner,
-		skillsSettings: settingsManager.getSkillsSettings(),
+		skillsSettings,
 		modelRegistry,
 		toolRegistry: wrappedToolRegistry ?? toolRegistry,
 		rebuildSystemPrompt,
diff --git a/packages/coding-agent/test/sdk-skills.test.ts b/packages/coding-agent/test/sdk-skills.test.ts
new file mode 100644
index 00000000..f8619dfa
--- /dev/null
+++ b/packages/coding-agent/test/sdk-skills.test.ts
@@ -0,0 +1,80 @@
+import { mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { createAgentSession } from "../src/core/sdk.js";
+import { SessionManager } from "../src/core/session-manager.js";
+
+describe("createAgentSession skills option", () => {
+	let tempDir: string;
+	let skillsDir: string;
+
+	beforeEach(() => {
+		tempDir = join(tmpdir(), `pi-sdk-test-${Date.now()}-${Math.random().toString(36).slice(2)}`);
+		skillsDir = join(tempDir, "skills", "test-skill");
+		mkdirSync(skillsDir, { recursive: true });
+
+		// Create a test skill
+		writeFileSync(
+			join(skillsDir, "SKILL.md"),
+			`---
+name: test-skill
+description: A test skill for SDK tests.
+---
+
+# Test Skill
+
+This is a test skill.
+`,
+		);
+	});
+
+	afterEach(() => {
+		if (tempDir) {
+			rmSync(tempDir, { recursive: true, force: true });
+		}
+	});
+
+	it("should discover skills by default", async () => {
+		const { session } = await createAgentSession({
+			cwd: tempDir,
+			agentDir: tempDir,
+			sessionManager: SessionManager.inMemory(),
+		});
+
+		// skillsSettings.enabled should be true (from default settings)
+		expect(session.skillsSettings?.enabled).toBe(true);
+	});
+
+	it("should disable skills in skillsSettings when options.skills is empty array", async () => {
+		const { session } = await createAgentSession({
+			cwd: tempDir,
+			agentDir: tempDir,
+			sessionManager: SessionManager.inMemory(),
+			skills: [], // Explicitly empty - like --no-skills
+		});
+
+		// skillsSettings.enabled should be false so UI doesn't re-discover
+		expect(session.skillsSettings?.enabled).toBe(false);
+	});
+
+	it("should disable skills in skillsSettings when options.skills is provided with skills", async () => {
+		const { session } = await createAgentSession({
+			cwd: tempDir,
+			agentDir: tempDir,
+			sessionManager: SessionManager.inMemory(),
+			skills: [
+				{
+					name: "custom-skill",
+					description: "A custom skill",
+					filePath: "/fake/path/SKILL.md",
+					baseDir: "/fake/path",
+					source: "custom",
+				},
+			],
+		});
+
+		// skillsSettings.enabled should be false because skills were explicitly provided
+		expect(session.skillsSettings?.enabled).toBe(false);
+	});
+});