diff --git a/packages/api/src/skills/parse.ts b/packages/api/src/skills/parse.ts
index 01e561f9f4..041e87ed5e 100644
--- a/packages/api/src/skills/parse.ts
+++ b/packages/api/src/skills/parse.ts
@@ -37,6 +37,10 @@ function getCaseInsensitive(frontmatter: Record<string, unknown>, key: string):
   return entry?.[1];
 }
 
+function hasCaseInsensitive(frontmatter: Record<string, unknown>, key: string): boolean {
+  return Object.keys(frontmatter).some((candidate) => candidate.toLowerCase() === key);
+}
+
 function getRawFrontmatterValue(block: string, key: string): string | undefined {
   const escapedKey = key.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
   const pattern = new RegExp(`^\\s*${escapedKey}\\s*:\\s*(.*)$`, 'i');
@@ -62,7 +66,8 @@ function stripInlineComment(value: string): string {
 
 function normalizeFrontmatterKeys(frontmatter: Record<string, unknown>): Record<string, unknown> {
   return Object.entries(frontmatter).reduce<Record<string, unknown>>((acc, [key, value]) => {
-    acc[key.toLowerCase()] = value;
+    const normalizedKey = key.toLowerCase();
+    acc[normalizedKey === 'alwaysapply' ? 'alwaysApply' : normalizedKey] = value;
     return acc;
   }, {});
 }
@@ -119,8 +124,12 @@ export function parseSkillMarkdown(raw: string): ParsedSkillMarkdown {
   const nameValue = getCaseInsensitive(frontmatter, 'name');
   const descriptionValue = getCaseInsensitive(frontmatter, 'description');
   const whenToUseValue = getCaseInsensitive(frontmatter, 'when-to-use');
-  const alwaysApplyValue = getCaseInsensitive(frontmatter, 'always-apply');
-  const rawAlwaysApplyValue = getRawFrontmatterValue(block, 'always-apply');
+  const hasCanonicalAlwaysApply = hasCaseInsensitive(frontmatter, 'always-apply');
+  const hasAliasAlwaysApply = hasCaseInsensitive(frontmatter, 'alwaysapply');
+  const canonicalAlwaysApplyValue = getCaseInsensitive(frontmatter, 'always-apply');
+  const aliasAlwaysApplyValue = getCaseInsensitive(frontmatter, 'alwaysapply');
+  const rawCanonicalAlwaysApplyValue = getRawFrontmatterValue(block, 'always-apply');
+  const rawAliasAlwaysApplyValue = getRawFrontmatterValue(block, 'alwaysApply');
   const name = toScalarString(nameValue);
   let description = '';
   if (descriptionValue !== undefined) {
@@ -130,11 +139,16 @@ export function parseSkillMarkdown(raw: string): ParsedSkillMarkdown {
   }
   let alwaysApply: boolean | undefined;
   const invalidBooleans: string[] = [];
-  if (alwaysApplyValue !== undefined) {
-    alwaysApply = parseBoolean(alwaysApplyValue, rawAlwaysApplyValue);
-    if (alwaysApply === undefined && !hasBooleanPlaceholder(rawAlwaysApplyValue)) {
+  if (hasCanonicalAlwaysApply) {
+    alwaysApply = parseBoolean(canonicalAlwaysApplyValue, rawCanonicalAlwaysApplyValue);
+    if (alwaysApply === undefined && !hasBooleanPlaceholder(rawCanonicalAlwaysApplyValue)) {
       invalidBooleans.push('always-apply');
     }
+  } else if (hasAliasAlwaysApply) {
+    alwaysApply = parseBoolean(aliasAlwaysApplyValue, rawAliasAlwaysApplyValue);
+    if (alwaysApply === undefined && !hasBooleanPlaceholder(rawAliasAlwaysApplyValue)) {
+      invalidBooleans.push('alwaysApply');
+    }
   }
   return {
     name,
diff --git a/packages/api/src/skills/sync/github.spec.ts b/packages/api/src/skills/sync/github.spec.ts
index 7cde5c9ad0..4f01dc8291 100644
--- a/packages/api/src/skills/sync/github.spec.ts
+++ b/packages/api/src/skills/sync/github.spec.ts
@@ -288,6 +288,24 @@ describe('createGitHubSkillSyncRunner', () => {
     );
   });
 
+  it('drops an invalid alwaysApply alias when canonical always-apply is valid', async () => {
+    const deps = createDeps({
+      fetchFn: githubFetch(
+        '---\nname: research\ndescription: Research things\nalways-apply: true\nalwaysApply: yes\n---\nBody',
+      ),
+    });
+    const runner = createGitHubSkillSyncRunner(deps);
+    const result = await runner.runOnce();
+
+    expect(result.status).toBe('completed');
+    expect(deps.createSkill).toHaveBeenCalledWith(
+      expect.objectContaining({
+        alwaysApply: true,
+        frontmatter: { 'always-apply': true },
+      }),
+    );
+  });
+
   it('discovers nested skill roots within the configured discovery depth', async () => {
     const skillMarkdown = '---\nname: tdd\ndescription: Test-driven development\n---\nBody';
     const fetchFn = jest.fn(async (input: RequestInfo | URL) => {
diff --git a/packages/api/src/skills/sync/github.ts b/packages/api/src/skills/sync/github.ts
index bbea40fee6..6887e18489 100644
--- a/packages/api/src/skills/sync/github.ts
+++ b/packages/api/src/skills/sync/github.ts
@@ -317,12 +317,18 @@ function toCleanFrontmatter(
   delete clean.name;
   delete clean.description;
   // Drop a placeholder/non-boolean always-apply (e.g. `always-apply:` or
-  // `always-apply: # TODO`, which js-yaml yields as null). The boolean is
-  // already captured in the dedicated alwaysApply field, and persisting a
-  // null here would leave ambiguous/invalid frontmatter on the synced skill.
+  // `always-apply: # TODO`, which js-yaml yields as null). Apply the same
+  // cleanup to the accepted `alwaysApply` alias so a malformed alias does not
+  // survive after the canonical key has already supplied the effective flag.
+  // The boolean is already captured in the dedicated alwaysApply field, and
+  // persisting a null here would leave ambiguous/invalid frontmatter on the
+  // synced skill.
   if ('always-apply' in clean && typeof clean['always-apply'] !== 'boolean') {
     delete clean['always-apply'];
   }
+  if ('alwaysApply' in clean && typeof clean.alwaysApply !== 'boolean') {
+    delete clean.alwaysApply;
+  }
   return clean;
 }