diff --git a/apps/server/src/provider/Layers/ClaudeProvider.ts b/apps/server/src/provider/Layers/ClaudeProvider.ts
index c6135fe247b..de317859807 100644
--- a/apps/server/src/provider/Layers/ClaudeProvider.ts
+++ b/apps/server/src/provider/Layers/ClaudeProvider.ts
@@ -29,6 +29,7 @@ import {
 import { compareCliVersions } from "../cliVersion.ts";
 import { makeManagedServerProvider } from "../makeManagedServerProvider.ts";
 import { ClaudeProvider } from "../Services/ClaudeProvider.ts";
+import { ServerConfig } from "../../config.ts";
 import { ServerSettingsService } from "../../serverSettings.ts";
 import { ServerSettingsError } from "@t3tools/contracts";
 
@@ -462,10 +463,16 @@ function dedupeSlashCommands(
  * after the local initialization phase completes. This gives us the
  * user's subscription type without incurring any token cost.
  *
+ * `cwd` determines how the SDK resolves the `"project"` and `"local"`
+ * setting sources, which is how project-level slash commands (including
+ * `.claude/skills/`) enter the initialization result. Pass the active
+ * project directory; otherwise the SDK falls back to the T3 server
+ * process cwd and project-level commands are missed (#2048).
+ *
  * This is used as a fallback when `claude auth status` does not include
  * subscription type information.
  */
-const probeClaudeCapabilities = (binaryPath: string) => {
+const probeClaudeCapabilities = (binaryPath: string, cwd?: string) => {
   const abort = new AbortController();
   return Effect.tryPromise(async () => {
     const q = claudeQuery({
@@ -473,6 +480,7 @@ const probeClaudeCapabilities = (binaryPath: string) => {
       options: {
         persistSession: false,
         pathToClaudeCodeExecutable: binaryPath,
+        ...(cwd ? { cwd } : {}),
         abortController: abort,
         maxTurns: 0,
         settingSources: ["user", "project", "local"],
@@ -759,25 +767,47 @@ const makePendingClaudeProvider = (claudeSettings: ClaudeSettings): ServerProvid
   });
 };
 
+/**
+ * Cache key for the Claude capability probe. `cwd` is included so probes
+ * from two different project directories stay in separate cache entries;
+ * a probe from `/repo-a` must not satisfy a probe for `/repo-b` because
+ * the SDK resolves `.claude/skills` against the provided cwd (#2048).
+ */
+export const claudeProbeCacheKey = (binaryPath: string, cwd?: string) =>
+  `${binaryPath}|${cwd ?? ""}`;
+
 export const ClaudeProviderLive = Layer.effect(
   ClaudeProvider,
   Effect.gen(function* () {
     const serverSettings = yield* ServerSettingsService;
     const spawner = yield* ChildProcessSpawner.ChildProcessSpawner;
-
+    // The active workspace the server was launched in. We pass this as the
+    // probe cwd so the Claude Agent SDK resolves `settingSources: ['project',
+    // 'local']` — and therefore `.claude/skills/` — against the user's
+    // project instead of the T3 server process cwd (#2048).
+    const { cwd: workspaceRoot } = yield* ServerConfig;
+
+    // Cache key is `${binaryPath}|${cwd ?? ''}` so probes with different
+    // project cwds don't collide. Capacity is 8 so a handful of recent
+    // projects stay cached without ballooning memory (#2048).
     const subscriptionProbeCache = yield* Cache.make({
-      capacity: 1,
+      capacity: 8,
       timeToLive: Duration.minutes(5),
-      lookup: (binaryPath: string) => probeClaudeCapabilities(binaryPath),
+      lookup: (key: string) => {
+        const sep = key.indexOf("|");
+        const binaryPath = sep >= 0 ? key.slice(0, sep) : key;
+        const cwd = sep >= 0 ? key.slice(sep + 1) : "";
+        return probeClaudeCapabilities(binaryPath, cwd || undefined);
+      },
     });
 
     const checkProvider = checkClaudeProviderStatus(
       (binaryPath) =>
-        Cache.get(subscriptionProbeCache, binaryPath).pipe(
+        Cache.get(subscriptionProbeCache, claudeProbeCacheKey(binaryPath, workspaceRoot)).pipe(
           Effect.map((probe) => probe?.subscriptionType),
         ),
       (binaryPath) =>
-        Cache.get(subscriptionProbeCache, binaryPath).pipe(
+        Cache.get(subscriptionProbeCache, claudeProbeCacheKey(binaryPath, workspaceRoot)).pipe(
           Effect.map((probe) => probe?.slashCommands),
         ),
     ).pipe(
diff --git a/apps/server/src/provider/Layers/ProviderRegistry.test.ts b/apps/server/src/provider/Layers/ProviderRegistry.test.ts
index 170521d2d27..eab76cb1b45 100644
--- a/apps/server/src/provider/Layers/ProviderRegistry.test.ts
+++ b/apps/server/src/provider/Layers/ProviderRegistry.test.ts
@@ -29,7 +29,11 @@ import {
   parseAuthStatusFromOutput,
   readCodexConfigModelProvider,
 } from "./CodexProvider.ts";
-import { checkClaudeProviderStatus, parseClaudeAuthStatusFromOutput } from "./ClaudeProvider.ts";
+import {
+  checkClaudeProviderStatus,
+  claudeProbeCacheKey,
+  parseClaudeAuthStatusFromOutput,
+} from "./ClaudeProvider.ts";
 import { haveProvidersChanged, ProviderRegistryLive } from "./ProviderRegistry.ts";
 import { ServerConfig } from "../../config.ts";
 import { ServerSettingsService, type ServerSettingsShape } from "../../serverSettings.ts";
@@ -1270,6 +1274,28 @@ it.layer(Layer.mergeAll(NodeServices.layer, ServerSettingsService.layerTest()))(
       );
     });
 
+    // ── claudeProbeCacheKey (per-cwd cache separation, #2048) ────────
+
+    describe("claudeProbeCacheKey", () => {
+      it("produces distinct keys for the same binary with different cwds", () => {
+        const a = claudeProbeCacheKey("/usr/local/bin/claude", "/repo-a");
+        const b = claudeProbeCacheKey("/usr/local/bin/claude", "/repo-b");
+        assert.notStrictEqual(a, b);
+      });
+
+      it("treats undefined and empty-string cwd as the same key", () => {
+        const undef = claudeProbeCacheKey("/usr/local/bin/claude");
+        const empty = claudeProbeCacheKey("/usr/local/bin/claude", "");
+        assert.strictEqual(undef, empty);
+      });
+
+      it("separates different binaries even with the same cwd", () => {
+        const a = claudeProbeCacheKey("/opt/claude-a", "/repo");
+        const b = claudeProbeCacheKey("/opt/claude-b", "/repo");
+        assert.notStrictEqual(a, b);
+      });
+    });
+
     // ── parseClaudeAuthStatusFromOutput pure tests ────────────────────
 
     describe("parseClaudeAuthStatusFromOutput", () => {