diff --git a/.changeset/spicy-laws-burn.md b/.changeset/spicy-laws-burn.md
new file mode 100644
index 0000000..05335ed
--- /dev/null
+++ b/.changeset/spicy-laws-burn.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/intent': patch
+---
+
+- Added Deno monorepo setup coverage so setup-github-actions writes workflows at the workspace root and preserves monorepo-aware path substitutions.
diff --git a/packages/intent/src/workspace-patterns.ts b/packages/intent/src/workspace-patterns.ts
index 8afa392..4c3d7d6 100644
--- a/packages/intent/src/workspace-patterns.ts
+++ b/packages/intent/src/workspace-patterns.ts
@@ -27,6 +27,101 @@ function hasPackageJson(dir: string): boolean {
   return existsSync(join(dir, 'package.json'))
 }
 
+function stripJsonCommentsAndTrailingCommas(source: string): string {
+  let result = ''
+  let inString = false
+  let escaped = false
+
+  for (let index = 0; index < source.length; index += 1) {
+    const char = source[index]!
+    const next = source[index + 1]
+
+    if (inString) {
+      result += char
+      if (escaped) {
+        escaped = false
+      } else if (char === '\\') {
+        escaped = true
+      } else if (char === '"') {
+        inString = false
+      }
+      continue
+    }
+
+    if (char === '"') {
+      inString = true
+      result += char
+      continue
+    }
+
+    if (char === '/' && next === '/') {
+      while (index < source.length && source[index] !== '\n') {
+        index += 1
+      }
+      if (index < source.length) {
+        result += source[index]!
+      }
+      continue
+    }
+
+    if (char === '/' && next === '*') {
+      const commentStart = index
+      index += 2
+      while (
+        index < source.length &&
+        !(source[index] === '*' && source[index + 1] === '/')
+      ) {
+        index += 1
+      }
+      if (index >= source.length) {
+        throw new SyntaxError(
+          `Unterminated block comment starting at position ${commentStart}`,
+        )
+      }
+      index += 1
+      continue
+    }
+
+    if (char === ',') {
+      let lookahead = index + 1
+      while (lookahead < source.length) {
+        const la = source[lookahead]!
+        if (/\s/.test(la)) {
+          lookahead += 1
+        } else if (la === '/' && source[lookahead + 1] === '/') {
+          lookahead += 2
+          while (lookahead < source.length && source[lookahead] !== '\n') {
+            lookahead += 1
+          }
+        } else if (la === '/' && source[lookahead + 1] === '*') {
+          lookahead += 2
+          while (
+            lookahead < source.length &&
+            !(source[lookahead] === '*' && source[lookahead + 1] === '/')
+          ) {
+            lookahead += 1
+          }
+          lookahead += 2
+        } else {
+          break
+        }
+      }
+      if (source[lookahead] === '}' || source[lookahead] === ']') {
+        continue
+      }
+    }
+
+    result += char
+  }
+
+  return result
+}
+
+function readJsonFile(path: string, jsonc = false): unknown {
+  const source = readFileSync(path, 'utf8')
+  return JSON.parse(jsonc ? stripJsonCommentsAndTrailingCommas(source) : source)
+}
+
 export function readWorkspacePatterns(root: string): Array<string> | null {
   const pnpmWs = join(root, 'pnpm-workspace.yaml')
   if (existsSync(pnpmWs)) {
@@ -40,8 +135,9 @@ export function readWorkspacePatterns(root: string): Array<string> | null {
         return patterns
       }
     } catch (err: unknown) {
+      const verb = err instanceof SyntaxError ? 'parse' : 'read'
       console.error(
-        `Warning: failed to parse ${pnpmWs}: ${err instanceof Error ? err.message : err}`,
+        `Warning: failed to ${verb} ${pnpmWs}: ${err instanceof Error ? err.message : err}`,
       )
     }
   }
@@ -49,16 +145,41 @@ export function readWorkspacePatterns(root: string): Array<string> | null {
   const pkgPath = join(root, 'package.json')
   if (existsSync(pkgPath)) {
     try {
-      const pkg = JSON.parse(readFileSync(pkgPath, 'utf8'))
+      const pkg = readJsonFile(pkgPath) as Record<string, unknown>
+      const workspaces = pkg.workspaces as Record<string, unknown> | undefined
       const patterns =
-        parseWorkspacePatterns(pkg.workspaces) ??
-        parseWorkspacePatterns(pkg.workspaces?.packages)
+        parseWorkspacePatterns(workspaces) ??
+        parseWorkspacePatterns(workspaces?.packages)
+      if (patterns) {
+        return patterns
+      }
+    } catch (err: unknown) {
+      const verb = err instanceof SyntaxError ? 'parse' : 'read'
+      console.error(
+        `Warning: failed to ${verb} ${pkgPath}: ${err instanceof Error ? err.message : err}`,
+      )
+    }
+  }
+
+  for (const denoConfigName of ['deno.json', 'deno.jsonc']) {
+    const denoConfigPath = join(root, denoConfigName)
+    if (!existsSync(denoConfigPath)) {
+      continue
+    }
+
+    try {
+      const denoConfig = readJsonFile(denoConfigPath, true) as Record<
+        string,
+        unknown
+      >
+      const patterns = parseWorkspacePatterns(denoConfig.workspace)
       if (patterns) {
         return patterns
       }
     } catch (err: unknown) {
+      const verb = err instanceof SyntaxError ? 'parse' : 'read'
       console.error(
-        `Warning: failed to parse ${pkgPath}: ${err instanceof Error ? err.message : err}`,
+        `Warning: failed to ${verb} ${denoConfigPath}: ${err instanceof Error ? err.message : err}`,
       )
     }
   }
diff --git a/packages/intent/tests/project-context.test.ts b/packages/intent/tests/project-context.test.ts
index c16b64e..0416d91 100644
--- a/packages/intent/tests/project-context.test.ts
+++ b/packages/intent/tests/project-context.test.ts
@@ -136,4 +136,31 @@ describe('resolveProjectContext', () => {
     expect(context.isMonorepo).toBe(true)
     expect(context.packageRoot).toBe(packageRoot)
   })
+
+  it('detects Deno workspaces from a workspace package cwd', () => {
+    const root = createRoot()
+    writeJson(join(root, 'package.json'), { name: 'repo-root', private: true })
+    writeFileSync(
+      join(root, 'deno.jsonc'),
+      `{
+        "workspace": [
+          "packages/*",
+        ],
+      }
+      `,
+    )
+    const packageRoot = createWorkspacePackage(root, 'router')
+
+    const context = resolveProjectContext({ cwd: packageRoot })
+
+    expect(context).toEqual({
+      cwd: packageRoot,
+      workspaceRoot: root,
+      packageRoot,
+      isMonorepo: true,
+      workspacePatterns: ['packages/*'],
+      targetPackageJsonPath: join(packageRoot, 'package.json'),
+      targetSkillsDir: join(packageRoot, 'skills'),
+    })
+  })
 })
diff --git a/packages/intent/tests/setup.test.ts b/packages/intent/tests/setup.test.ts
index 6911a8c..181cff6 100644
--- a/packages/intent/tests/setup.test.ts
+++ b/packages/intent/tests/setup.test.ts
@@ -344,6 +344,72 @@ describe('runSetupGithubActions', () => {
 
     rmSync(monoRoot, { recursive: true, force: true })
   })
+
+  it('writes workflows to the Deno workspace root from a workspace package', () => {
+    const monoRoot = createMonorepo({
+      usePackageJsonWorkspaces: true,
+      packages: [
+        { name: 'router', hasSkills: true },
+        { name: 'start', hasSkills: true },
+      ],
+    })
+
+    writeFileSync(
+      join(monoRoot, 'package.json'),
+      JSON.stringify({ name: 'root', private: true }, null, 2),
+    )
+    writeFileSync(
+      join(monoRoot, 'deno.jsonc'),
+      `{
+        // Deno workspace config should be used for monorepo resolution.
+        "workspace": [
+          "packages/*",
+        ],
+      }
+      `,
+    )
+    writeFileSync(
+      join(monoRoot, 'packages', 'router', 'package.json'),
+      JSON.stringify(
+        {
+          name: '@tanstack/react-router',
+          intent: { repo: 'TanStack/router', docs: 'docs/' },
+        },
+        null,
+        2,
+      ),
+    )
+    mkdirSync(join(monoRoot, 'packages', 'router', 'src'), { recursive: true })
+    mkdirSync(join(monoRoot, 'packages', 'router', 'docs'), { recursive: true })
+    mkdirSync(join(monoRoot, 'packages', 'start', 'src'), { recursive: true })
+
+    const result = runSetupGithubActions(
+      join(monoRoot, 'packages', 'router'),
+      metaDir,
+    )
+
+    expect(result.workflows).toEqual(
+      expect.arrayContaining([
+        join(monoRoot, '.github', 'workflows', 'notify-intent.yml'),
+        join(monoRoot, '.github', 'workflows', 'check-skills.yml'),
+      ]),
+    )
+    expect(
+      existsSync(join(monoRoot, 'packages', 'router', '.github', 'workflows')),
+    ).toBe(false)
+
+    const notifyContent = readFileSync(
+      join(monoRoot, '.github', 'workflows', 'notify-intent.yml'),
+      'utf8',
+    )
+    expect(notifyContent).toContain('package: @tanstack/router')
+    expect(notifyContent).toContain('repo: TanStack/router')
+    expect(notifyContent).toContain("- 'packages/router/docs/**'")
+    expect(notifyContent).toContain("- 'packages/router/src/**'")
+    expect(notifyContent).toContain("- 'packages/start/src/**'")
+
+    rmSync(monoRoot, { recursive: true, force: true })
+  })
 })
 
 // ---------------------------------------------------------------------------
diff --git a/packages/intent/tests/workspace-patterns.test.ts b/packages/intent/tests/workspace-patterns.test.ts
index e48f646..15f3fdd 100644
--- a/packages/intent/tests/workspace-patterns.test.ts
+++ b/packages/intent/tests/workspace-patterns.test.ts
@@ -7,7 +7,7 @@ import {
 } from 'node:fs'
 import { join } from 'node:path'
 import { tmpdir } from 'node:os'
-import { afterEach, describe, expect, it } from 'vitest'
+import { afterEach, describe, expect, it, vi } from 'vitest'
 import {
   findPackagesWithSkills,
   findWorkspaceRoot,
@@ -78,6 +78,70 @@ describe('readWorkspacePatterns', () => {
       'packages/*',
     ])
   })
+
+  it('reads workspace patterns from deno.json', () => {
+    const root = createRoot()
+
+    writeFileSync(
+      join(root, 'deno.json'),
+      JSON.stringify({
+        workspace: ['', './apps/*/', 'packages\\*', 'apps/*'],
+      }),
+    )
+
+    expect(readWorkspacePatterns(root)).toEqual(['apps/*', 'packages/*'])
+  })
+
+  it('reads workspace patterns from deno.jsonc', () => {
+    const root = createRoot()
+
+    writeFileSync(
+      join(root, 'deno.jsonc'),
+      `{
+        // Deno supports JSONC config files.
+        "workspace": [
+          "./packages/*/",
+          "apps/*",
+        ],
+      }
+      `,
+    )
+
+    expect(readWorkspacePatterns(root)).toEqual(['apps/*', 'packages/*'])
+  })
+
+  it('prefers package.json workspaces over Deno workspace config', () => {
+    const root = createRoot()
+
+    writeFileSync(
+      join(root, 'package.json'),
+      JSON.stringify({ workspaces: ['packages/*'] }),
+    )
+    writeFileSync(
+      join(root, 'deno.json'),
+      JSON.stringify({ workspace: ['apps/*'] }),
+    )
+
+    expect(readWorkspacePatterns(root)).toEqual(['packages/*'])
+  })
+
+  it('warns and returns null for invalid Deno config', () => {
+    const root = createRoot()
+    const consoleErrorSpy = vi
+      .spyOn(console, 'error')
+      .mockImplementation(() => undefined)
+
+    writeFileSync(join(root, 'deno.jsonc'), '{ invalid jsonc')
+
+    expect(readWorkspacePatterns(root)).toBeNull()
+    expect(consoleErrorSpy).toHaveBeenCalledWith(
+      expect.stringContaining(
+        `Warning: failed to parse ${join(root, 'deno.jsonc')}`,
+      ),
+    )
+
+    consoleErrorSpy.mockRestore()
+  })
 })
 
 describe('resolveWorkspacePackages', () => {