diff --git a/.changeset/bundle-skills-single-pass.md b/.changeset/bundle-skills-single-pass.md
new file mode 100644
index 00000000000..30b2c428b22
--- /dev/null
+++ b/.changeset/bundle-skills-single-pass.md
@@ -0,0 +1,5 @@
+---
+"trigger.dev": patch
+---
+
+Fix `chat.agent` skills silently missing in `trigger dev` for projects whose task files read `process.env` at module top level (e.g. a third-party SDK client initialized at import). Skill folders now bundle into `.trigger/skills/` reliably regardless of which env vars are set when the CLI launches.
diff --git a/packages/cli-v3/src/build/bundleSkills.ts b/packages/cli-v3/src/build/bundleSkills.ts
index 65ad9834abe..8533d254c72 100644
--- a/packages/cli-v3/src/build/bundleSkills.ts
+++ b/packages/cli-v3/src/build/bundleSkills.ts
@@ -1,6 +1,5 @@
-import { createHash } from "node:crypto";
 import { readFile } from "node:fs/promises";
-import { dirname, isAbsolute, join, resolve as resolvePath } from "node:path";
+import { isAbsolute, join, resolve as resolvePath } from "node:path";
 import type { BuildManifest, SkillManifest } from "@trigger.dev/core/v3/schemas";
 import { copyDirectoryRecursive } from "@trigger.dev/build/internal";
 import { indexWorkerManifest } from "../indexing/indexWorkerManifest.js";
@@ -21,13 +20,84 @@ export type BundleSkillsResult = {
   skills: SkillManifest[];
 };
 
+export type CopySkillFoldersOptions = {
+  skills: SkillManifest[];
+  /** Root where `{destinationRoot}/{id}/` folders will be created. */
+  destinationRoot: string;
+  /** Used to resolve relative `filePath` references in skill manifests. */
+  workingDir: string;
+  /** Only `debug` is used. `BuildLogger` and the cli `logger` both satisfy this shape. */
+  logger: { debug: (...args: unknown[]) => void };
+};
+
+/**
+ * Copy each skill's source folder to `{destinationRoot}/{id}/`. Validates
+ * that `SKILL.md` exists and has the required frontmatter. Pure file IO —
+ * no indexer subprocess, no env handling.
+ *
+ * Used by the dev path (driven by the main worker indexer's skills list)
+ * and indirectly by the deploy path (via `bundleSkills` which discovers
+ * skills via its own indexer pass first, then delegates here).
+ */
+export async function copySkillFolders(
+  options: CopySkillFoldersOptions
+): Promise<SkillManifest[]> {
+  const { skills, destinationRoot, workingDir, logger } = options;
+
+  if (skills.length === 0) {
+    return [];
+  }
+
+  for (const skill of skills) {
+    const callerDir = skill.filePath
+      ? resolvePath(workingDir, skill.filePath, "..")
+      : workingDir;
+    const sourcePath = isAbsolute(skill.sourcePath)
+      ? skill.sourcePath
+      : resolvePath(callerDir, skill.sourcePath);
+    const skillMdPath = join(sourcePath, "SKILL.md");
+
+    let skillMd: string;
+    try {
+      skillMd = await readFile(skillMdPath, "utf8");
+    } catch {
+      throw new Error(
+        `Skill "${skill.id}": SKILL.md not found at ${skillMdPath}. ` +
+          `Registered via skills.define({ id: "${skill.id}", path: "${skill.sourcePath}" }) ` +
+          `at ${skill.filePath}.`
+      );
+    }
+
+    if (!/^---\r?\n[\s\S]*?\r?\n---/.test(skillMd)) {
+      throw new Error(
+        `Skill "${skill.id}": SKILL.md at ${skillMdPath} is missing a frontmatter block.`
+      );
+    }
+    if (!/\bname:\s*\S/.test(skillMd) || !/\bdescription:\s*\S/.test(skillMd)) {
+      throw new Error(
+        `Skill "${skill.id}": SKILL.md at ${skillMdPath} frontmatter must include both \`name\` and \`description\`.`
+      );
+    }
+
+    const skillDest = join(destinationRoot, skill.id);
+    logger.debug(`[copySkillFolders] Copying ${sourcePath} → ${skillDest}`);
+    await copyDirectoryRecursive(sourcePath, skillDest);
+  }
+
+  return [...skills].sort((a, b) => a.id.localeCompare(b.id));
+}
+
 /**
  * Built-in skill bundler — not an extension. Runs the indexer locally
- * against the bundled worker output to discover `ai.defineSkill(...)`
+ * against the bundled worker output to discover `skills.define(...)`
  * registrations, validates each skill's `SKILL.md`, and copies the
  * folder into `{outputPath}/.trigger/skills/{id}/` so the deploy image
  * picks it up via the existing Dockerfile `COPY`.
  *
+ * Used by the deploy path. The dev path uses `copySkillFolders` directly,
+ * driven by the main worker indexer that already runs in `BackgroundWorker.initialize` —
+ * no duplicate indexer pass needed there.
+ *
  * No `trigger.config.ts` changes required — discovery is side-effect
  * based, same mechanism as task/prompt registration.
  */
@@ -71,65 +141,20 @@ export async function bundleSkills(
     return { buildManifest, skills: [] };
   }
 
-  // Destination layout differs between dev and deploy:
-  // - Dev:    the worker runs with cwd = workingDir, so skills must live at
-  //           {workingDir}/.trigger/skills/{id}/ for skill.local() to find them.
-  // - Deploy: the Dockerfile COPY picks up everything under outputPath into
-  //           /app, so we target {outputPath}/.trigger/skills/{id}/ and the
-  //           container's cwd (/app) resolves correctly.
-  const destinationRoot =
-    buildManifest.target === "dev"
-      ? join(workingDir, ".trigger", "skills")
-      : join(buildManifest.outputPath, ".trigger", "skills");
+  // Deploy target: the Dockerfile COPY picks up everything under outputPath
+  // into /app, so we target {outputPath}/.trigger/skills/{id}/ and the
+  // container's cwd (/app) resolves correctly.
+  const destinationRoot = join(buildManifest.outputPath, ".trigger", "skills");
 
-  for (const skill of skills) {
-    // Resolve the skill's source folder relative to the file that called
-    // `skills.define(...)`. Absolute paths are honored as-is.
-    const callerDir = skill.filePath
-      ? dirname(resolvePath(workingDir, skill.filePath))
-      : workingDir;
-    const sourcePath = isAbsolute(skill.sourcePath)
-      ? skill.sourcePath
-      : resolvePath(callerDir, skill.sourcePath);
-    const skillMdPath = join(sourcePath, "SKILL.md");
-
-    let skillMd: string;
-    try {
-      skillMd = await readFile(skillMdPath, "utf8");
-    } catch {
-      throw new Error(
-        `Skill "${skill.id}": SKILL.md not found at ${skillMdPath}. ` +
-          `Registered via ai.defineSkill({ id: "${skill.id}", path: "${skill.sourcePath}" }) ` +
-          `at ${skill.filePath}.`
-      );
-    }
-
-    if (!/^---\r?\n[\s\S]*?\r?\n---/.test(skillMd)) {
-      throw new Error(
-        `Skill "${skill.id}": SKILL.md at ${skillMdPath} is missing a frontmatter block.`
-      );
-    }
-    if (!/\bname:\s*\S/.test(skillMd) || !/\bdescription:\s*\S/.test(skillMd)) {
-      throw new Error(
-        `Skill "${skill.id}": SKILL.md at ${skillMdPath} frontmatter must include both \`name\` and \`description\`.`
-      );
-    }
-
-    const skillDest = join(destinationRoot, skill.id);
-    logger.debug(`[bundleSkills] Copying ${sourcePath} → ${skillDest}`);
-    await copyDirectoryRecursive(sourcePath, skillDest);
-  }
-
-  // Sort by id for deterministic manifest output
-  skills = [...skills].sort((a, b) => a.id.localeCompare(b.id));
-
-  // Content hash is derived from each SKILL.md's content for cache invalidation
-  // downstream (dashboard persistence in Phase 2). Not used in Phase 1.
-  void createHash;
-  void dirname;
+  const sortedSkills = await copySkillFolders({
+    skills,
+    destinationRoot,
+    workingDir,
+    logger,
+  });
 
   return {
-    buildManifest: { ...buildManifest, skills },
-    skills,
+    buildManifest: { ...buildManifest, skills: sortedSkills },
+    skills: sortedSkills,
   };
 }
diff --git a/packages/cli-v3/src/dev/devSession.ts b/packages/cli-v3/src/dev/devSession.ts
index 2d6645cd50c..ed6290a1b86 100644
--- a/packages/cli-v3/src/dev/devSession.ts
+++ b/packages/cli-v3/src/dev/devSession.ts
@@ -9,7 +9,6 @@ import {
   logBuildFailure,
   logBuildWarnings,
 } from "../build/bundle.js";
-import { bundleSkills } from "../build/bundleSkills.js";
 import {
   createBuildContext,
   notifyExtensionOnBuildComplete,
@@ -119,25 +118,12 @@ export async function startDevSession({
       bundle.metafile
     );
 
-    // Built-in skill bundling — copies registered skill folders into
-    // `.trigger/skills/{id}/` so `skill.local()` works at dev runtime.
-    try {
-      const buildManifestPath = join(
-        workerDir?.path ?? destination.path,
-        "build.json"
-      );
-      await writeJSONFile(buildManifestPath, buildManifest);
-      const skillsResult = await bundleSkills({
-        buildManifest,
-        buildManifestPath,
-        workingDir: rawConfig.workingDir,
-        env: process.env,
-        logger: buildContext.logger,
-      });
-      buildManifest = skillsResult.buildManifest;
-    } catch (err) {
-      logger.warn("Skill bundling failed during dev rebuild", err);
-    }
+    // Skill folder copying happens after the main worker indexer runs in
+    // `BackgroundWorker.initialize` — that pass already discovers skills
+    // via the resource catalog and reports them on `workerManifest.skills`,
+    // so we don't need a duplicate indexer here (which historically ran
+    // with a bare `process.env` and silently dropped skills on projects
+    // whose task files read CLI-injected vars at module top level).
 
     buildManifest = await notifyExtensionOnBuildComplete(buildContext, buildManifest);
 
diff --git a/packages/cli-v3/src/dev/devSupervisor.ts b/packages/cli-v3/src/dev/devSupervisor.ts
index 59b2d2a473b..0d972384c40 100644
--- a/packages/cli-v3/src/dev/devSupervisor.ts
+++ b/packages/cli-v3/src/dev/devSupervisor.ts
@@ -18,6 +18,7 @@ import { eventBus } from "../utilities/eventBus.js";
 import { logger } from "../utilities/logger.js";
 import { resolveSourceFiles } from "../utilities/sourceFiles.js";
 import { BackgroundWorker } from "./backgroundWorker.js";
+import { copySkillFolders } from "../build/bundleSkills.js";
 import { WorkerRuntime } from "./workerRuntime.js";
 import { chalkTask, cliLink, prettyError } from "../utilities/cliOutput.js";
 import { DevRunController } from "../entryPoints/dev-run-controller.js";
@@ -331,6 +332,25 @@ class DevSupervisor implements WorkerRuntime {
       throw new Error("Could not initialize worker");
     }
 
+    // Copy registered skill folders into `${workingDir}/.trigger/skills/{id}/`
+    // so `skill.local()` can read them at runtime. The main indexer already
+    // discovered skills; we just do the file IO here.
+    const discoveredSkills = backgroundWorker.manifest.skills ?? [];
+    if (discoveredSkills.length > 0) {
+      try {
+        await copySkillFolders({
+          skills: discoveredSkills,
+          destinationRoot: join(this.options.config.workingDir, ".trigger", "skills"),
+          workingDir: this.options.config.workingDir,
+          logger,
+        });
+      } catch (err) {
+        prettyError("Skill bundling failed", (err as Error).message);
+        stop();
+        return;
+      }
+    }
+
     const validationIssue = validateWorkerManifest(backgroundWorker.manifest);
 
     if (validationIssue) {
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 17f73d9a252..d0bb1e5b836 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -2223,6 +2223,19 @@ importers:
         specifier: 3.25.76
         version: 3.25.76
 
+  references/agent-skills:
+    dependencies:
+      '@trigger.dev/build':
+        specifier: workspace:*
+        version: link:../../packages/build
+      '@trigger.dev/sdk':
+        specifier: workspace:*
+        version: link:../../packages/trigger-sdk
+    devDependencies:
+      trigger.dev:
+        specifier: workspace:*
+        version: link:../../packages/cli-v3
+
   references/ai-chat:
     dependencies:
       '@ai-sdk/anthropic':
diff --git a/references/agent-skills/package.json b/references/agent-skills/package.json
new file mode 100644
index 00000000000..b8016c09279
--- /dev/null
+++ b/references/agent-skills/package.json
@@ -0,0 +1,16 @@
+{
+  "name": "references-agent-skills",
+  "private": true,
+  "type": "module",
+  "devDependencies": {
+    "trigger.dev": "workspace:*"
+  },
+  "dependencies": {
+    "@trigger.dev/build": "workspace:*",
+    "@trigger.dev/sdk": "workspace:*"
+  },
+  "scripts": {
+    "dev": "trigger dev",
+    "deploy": "trigger deploy"
+  }
+}
diff --git a/references/agent-skills/src/trigger/skills/greeter/SKILL.md b/references/agent-skills/src/trigger/skills/greeter/SKILL.md
new file mode 100644
index 00000000000..a824f138003
--- /dev/null
+++ b/references/agent-skills/src/trigger/skills/greeter/SKILL.md
@@ -0,0 +1,18 @@
+---
+name: greeter
+description: Say hello in different styles. Use when the user asks for a greeting or a friendly message.
+---
+
+# Greeter
+
+A tiny skill used to validate that the CLI bundles `SKILL.md` plus a `scripts/` subfolder into the deploy image and that `skill.local()` can read both at runtime.
+
+## When to use
+
+- Anyone asks for "hello" — invoke `scripts/hello.sh [NAME]` and return its stdout.
+
+## Scripts
+
+### `scripts/hello.sh [NAME]`
+
+Prints `Hello, {NAME}!` (default `world`). Used to confirm `scripts/` is copied alongside `SKILL.md`.
diff --git a/references/agent-skills/src/trigger/skills/greeter/scripts/hello.sh b/references/agent-skills/src/trigger/skills/greeter/scripts/hello.sh
new file mode 100755
index 00000000000..b94fa92f76a
--- /dev/null
+++ b/references/agent-skills/src/trigger/skills/greeter/scripts/hello.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+NAME="${1:-world}"
+echo "Hello, ${NAME}!"
diff --git a/references/agent-skills/src/trigger/test-skill.ts b/references/agent-skills/src/trigger/test-skill.ts
new file mode 100644
index 00000000000..6a6de46665d
--- /dev/null
+++ b/references/agent-skills/src/trigger/test-skill.ts
@@ -0,0 +1,42 @@
+import { logger, skills, task } from "@trigger.dev/sdk";
+import { exec } from "node:child_process";
+import { promisify } from "node:util";
+import { join } from "node:path";
+import { access, constants } from "node:fs/promises";
+
+const greeterSkill = skills.define({
+  id: "greeter",
+  path: "./skills/greeter",
+});
+
+const execAsync = promisify(exec);
+
+export const testSkillTask = task({
+  id: "test-skill",
+  run: async (payload: { name?: string } = {}) => {
+    const resolved = await greeterSkill.local();
+
+    logger.info("Resolved skill", {
+      id: resolved.id,
+      version: resolved.version,
+      path: resolved.path,
+      frontmatterName: resolved.frontmatter.name,
+      frontmatterDescription: resolved.frontmatter.description,
+      bodyChars: resolved.body.length,
+    });
+
+    const scriptPath = join(resolved.path, "scripts", "hello.sh");
+    await access(scriptPath, constants.X_OK);
+
+    const { stdout } = await execAsync(`bash ${scriptPath} ${payload.name ?? "world"}`);
+    const output = stdout.trim();
+    logger.info("Script output", { output });
+
+    return {
+      skillId: resolved.id,
+      skillPath: resolved.path,
+      frontmatterName: resolved.frontmatter.name,
+      scriptOutput: output,
+    };
+  },
+});
diff --git a/references/agent-skills/trigger.config.ts b/references/agent-skills/trigger.config.ts
new file mode 100644
index 00000000000..5a5c9779107
--- /dev/null
+++ b/references/agent-skills/trigger.config.ts
@@ -0,0 +1,9 @@
+import { defineConfig } from "@trigger.dev/sdk";
+
+export default defineConfig({
+  project: "proj_zweffkxiuovfzsdtjvbe",
+  runtime: "node",
+  logLevel: "info",
+  maxDuration: 60,
+  dirs: ["./src/trigger"],
+});
diff --git a/references/agent-skills/tsconfig.json b/references/agent-skills/tsconfig.json
new file mode 100644
index 00000000000..2ca0ae6e2d7
--- /dev/null
+++ b/references/agent-skills/tsconfig.json
@@ -0,0 +1,13 @@
+{
+  "compilerOptions": {
+    "target": "ES2023",
+    "module": "Node16",
+    "moduleResolution": "Node16",
+    "esModuleInterop": true,
+    "strict": true,
+    "skipLibCheck": true,
+    "customConditions": ["@triggerdotdev/source"],
+    "noEmit": true
+  },
+  "include": ["./src/**/*.ts", "trigger.config.ts"]
+}