diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 631b88d16..3621d3150 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -29,6 +29,7 @@
 - Fixed runs started by `pi.sendMessage(..., { triggerTurn: true })` removing system prompt sections added in `before_agent_start` after their first tool call, which changed the prompt mid-run and broke the provider prompt cache twice per run ([#10267](https://github.com/earendil-works/pi/issues/10267))
 - Fixed codemode blocking the process for seconds to minutes after scripts with many `text()` calls; joining the output items was quadratic ([#10678](https://github.com/earendil-works/pi/issues/10678))
 - Fixed `pi mcp login --help` and the CLI docs describing `--timeout` as only the wait for the browser; it limits the whole sign-in ([#10636](https://github.com/earendil-works/pi/issues/10636))
+- Fixed `~` not being expanded in `!pattern`, `+path`, and `-path` entries of the `extensions`, `skills`, `prompts`, and `themes` settings, so entries like `!~/skills/pdf` matched nothing ([#10765](https://github.com/earendil-works/pi/issues/10765))
 
 ### Removed
 
diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index b5bb19d74..1ca63ebbb 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -40,7 +40,13 @@ import { gt, maxSatisfying, rcompare, satisfies, valid, validRange } from "semve
 import { CONFIG_DIR_NAME } from "../config.ts";
 import { spawnProcess, spawnProcessSync } from "../utils/child-process.ts";
 import { type GitSource, parseGitUrl } from "../utils/git.ts";
-import { canonicalizePath, isLocalPath, markPathIgnoredByCloudSync, resolvePath } from "../utils/paths.ts";
+import {
+	canonicalizePath,
+	isLocalPath,
+	markPathIgnoredByCloudSync,
+	normalizePath,
+	resolvePath,
+} from "../utils/paths.ts";
 import { stripBom } from "../utils/text.ts";
 import { isStdoutTakenOver } from "./output-guard.ts";
 import { type PiManifest, readPiManifest } from "./pi-manifest.ts";
@@ -669,7 +675,7 @@ function matchesAnyPattern(filePath: string, patterns: string[], baseDir: string
 	const parentDirPosix = isSkillFile ? toPosixPath(parentDir!) : undefined;
 
 	return patterns.some((pattern) => {
-		const normalizedPattern = toPosixPath(pattern);
+		const normalizedPattern = toPosixPath(normalizePath(pattern));
 		if (
 			minimatch(rel, normalizedPattern) ||
 			minimatch(name, normalizedPattern) ||
@@ -688,7 +694,7 @@ function matchesAnyPattern(filePath: string, patterns: string[], baseDir: string
 
 function normalizeExactPattern(pattern: string): string {
 	const normalized = pattern.startsWith("./") || pattern.startsWith(".\\") ? pattern.slice(2) : pattern;
-	return toPosixPath(normalized);
+	return toPosixPath(normalizePath(normalized));
 }
 
 function matchesAnyExactPattern(filePath: string, patterns: string[], baseDir: string): boolean {
diff --git a/packages/coding-agent/test/package-manager.test.ts b/packages/coding-agent/test/package-manager.test.ts
index a81054bbe..8aedd93c4 100644
--- a/packages/coding-agent/test/package-manager.test.ts
+++ b/packages/coding-agent/test/package-manager.test.ts
@@ -1612,6 +1612,37 @@ Content`,
 	});
 
 	describe("pattern filtering in top-level arrays", () => {
+		// #10765
+		it("should expand ~ in exclusion and exact patterns", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const skillsDir = join(tempDir, "extra", "skills");
+				for (const name of ["keep", "glob-excluded", "exact-excluded"]) {
+					mkdirSync(join(skillsDir, name), { recursive: true });
+					writeFileSync(join(skillsDir, name, "SKILL.md"), `---\nname: ${name}\ndescription: ${name}\n---\n`);
+				}
+
+				settingsManager.setSkillPaths([
+					"~/extra/skills",
+					"!~/extra/skills/glob-*",
+					"-~/extra/skills/exact-excluded",
+				]);
+
+				const result = await packageManager.resolve();
+				expect(result.skills.some((r) => isEnabled(r, "keep/SKILL.md"))).toBe(true);
+				expect(result.skills.some((r) => isDisabled(r, "glob-excluded/SKILL.md"))).toBe(true);
+				expect(result.skills.some((r) => isDisabled(r, "exact-excluded/SKILL.md"))).toBe(true);
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
+
 		it("should exclude extensions with ! pattern", async () => {
 			const extDir = join(agentDir, "extensions");
 			mkdirSync(extDir, { recursive: true });