diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index b65ff1a6..30902977 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+### Fixed
+
+- Fixed `pi config` misclassifying `~/.agents/skills` as project-scoped in non-git directories under `$HOME`, so toggling those skills no longer writes project overrides to `.pi/settings.json` ([#1915](https://github.com/badlogic/pi-mono/issues/1915))
+
 ## [0.56.3] - 2026-03-06
 
 ### New Features
diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index 43240821..48375820 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -1607,7 +1607,9 @@ export class DefaultPackageManager implements PackageManager {
 			themes: join(projectBaseDir, "themes"),
 		};
 		const userAgentsSkillsDir = join(homedir(), ".agents", "skills");
-		const projectAgentsSkillDirs = collectAncestorAgentsSkillDirs(this.cwd);
+		const projectAgentsSkillDirs = collectAncestorAgentsSkillDirs(this.cwd).filter(
+			(dir) => resolve(dir) !== resolve(userAgentsSkillsDir),
+		);
 
 		const addResources = (
 			resourceType: ResourceType,
diff --git a/packages/coding-agent/test/package-manager.test.ts b/packages/coding-agent/test/package-manager.test.ts
index f427b339..91ec5955 100644
--- a/packages/coding-agent/test/package-manager.test.ts
+++ b/packages/coding-agent/test/package-manager.test.ts
@@ -213,6 +213,42 @@ Content`,
 			expect(result.skills.some((r) => r.path === rootSkill && r.enabled)).toBe(true);
 			expect(result.skills.some((r) => r.path === middleSkill && r.enabled)).toBe(true);
 		});
+
+		it("should keep ~/.agents/skills user-scoped when cwd is under home in a non-git directory", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const cwd = join(tempDir, "scratch", "nested");
+				const localAgentDir = join(tempDir, ".pi", "agent");
+				const localSettingsManager = SettingsManager.inMemory();
+				mkdirSync(cwd, { recursive: true });
+				mkdirSync(localAgentDir, { recursive: true });
+
+				const homeSkill = join(tempDir, ".agents", "skills", "home-skill", "SKILL.md");
+				mkdirSync(join(tempDir, ".agents", "skills", "home-skill"), { recursive: true });
+				writeFileSync(homeSkill, "---\nname: home-skill\ndescription: home\n---\n");
+
+				const pm = new DefaultPackageManager({
+					cwd,
+					agentDir: localAgentDir,
+					settingsManager: localSettingsManager,
+				});
+
+				const result = await pm.resolve();
+				const matchingSkills = result.skills.filter((r) => r.path === homeSkill);
+				expect(matchingSkills).toHaveLength(1);
+				expect(matchingSkills[0]?.enabled).toBe(true);
+				expect(matchingSkills[0]?.metadata.scope).toBe("user");
+				expect(matchingSkills[0]?.metadata.source).toBe("auto");
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
 	});
 
 	describe("ignore files", () => {