diff --git a/package.json b/package.json
index 6198c1999..88fdcb4b3 100644
--- a/package.json
+++ b/package.json
@@ -229,6 +229,7 @@
     "test:evidence-bundle-digest-and-recipe-artifact": "tsx tests/evidence-bundle-digest-and-recipe-artifact.test.ts",
     "test:runtime-overlay-descriptors": "tsx tests/runtime-overlay-descriptors.test.ts",
     "test:composer-package-overlay-revision": "tsx scripts/composer-backed-source-hydration-smoke.ts",
+    "test:composer-package-overlay-autoload-layout": "tsx scripts/composer-package-overlay-autoload-layout-smoke.ts",
     "test:composer-installed-versions-loader-order": "tsx scripts/composer-installed-versions-loader-order-smoke.ts",
     "test:runtime-preset-registry": "tsx tests/runtime-preset-registry.test.ts",
     "test:generic-ability-runtime-run": "tsx tests/generic-ability-runtime-run.test.ts",
diff --git a/packages/cli/src/recipe-sources.ts b/packages/cli/src/recipe-sources.ts
index ec20c9668..5058374ad 100644
--- a/packages/cli/src/recipe-sources.ts
+++ b/packages/cli/src/recipe-sources.ts
@@ -454,7 +454,18 @@ async function prepareRecipeDependencyOverlay(overlay: WorkspaceRecipeDependency
   await validateExistingDirectoryForOverlay(source, overlay.source)
   const reference = await resolvedGitSourceReference(source)
   const stagingRoot = await mkdtemp(join(tmpdir(), "wp-codebox-dependency-overlay-"))
-  const preparedSource = await prepareComposerBackedSource(source, stagingRoot, `dependency overlay ${overlay.package}`)
+  const hydratedSource = await prepareComposerBackedSource(source, stagingRoot, `dependency overlay ${overlay.package}`)
+  // The overlay is mounted at the consumer's vendor path for the package and is
+  // autoloaded through the consumer's committed PSR-4 map, not the override's
+  // own. When the consumer records the package under a different PSR-4 source
+  // layout than the override ships (e.g. a repo that publishes `src/` but is
+  // consumed as `php-transformer/src/`), the mounted class files would sit where
+  // the consumer autoloader never looks and the override is silently ignored.
+  // Reconcile the staged source so each namespace's classes land at the path the
+  // consumer's autoloader resolves, keeping the single vendor-path mount intact.
+  // Never mutate the caller's checkout: stage a copy first when the hydrated
+  // source is still the original directory.
+  const preparedSource = await reconcileOverlayAutoloadLayout(hydratedSource, source, stagingRoot, consumer.source, overlay.package)
   if (reference) {
     await preserveComposerDependencyReference(consumer, overlay.package, reference, stagedConsumers)
     await preserveComposerPackageReference(preparedSource, overlay.package, reference)
@@ -487,6 +498,108 @@ async function prepareRecipeDependencyOverlay(overlay: WorkspaceRecipeDependency
   }
 }
 
+/**
+ * Move the overlay's PSR-4 source directories to the paths the consumer's
+ * committed autoloader resolves for the same package. The overlay is mounted at
+ * the consumer's `vendor/<package>` path and loaded via the consumer's PSR-4
+ * map; when the override ships a different source layout than the consumer
+ * recorded (e.g. `src/` vs `php-transformer/src/`), the mounted classes must be
+ * relocated to the consumer's recorded layout or they are never autoloaded.
+ */
+async function reconcileOverlayAutoloadLayout(hydratedSource: string, originalSource: string, stagingRoot: string, consumerSource: string, packageName: string): Promise<string> {
+  const consumerPsr4 = await composerPackagePsr4FromInstalled(join(consumerSource, "vendor", "composer", "installed.json"), packageName)
+  const overridePsr4 = await composerPackagePsr4FromInstalled(join(hydratedSource, "vendor", "composer", "installed.json"), packageName)
+    ?? await composerPackagePsr4FromComposerJson(join(hydratedSource, "composer.json"))
+  if (!consumerPsr4 || !overridePsr4) {
+    return hydratedSource
+  }
+
+  const moves = new Map<string, string>()
+  for (const [namespace, consumerDir] of Object.entries(consumerPsr4)) {
+    const overrideDir = overridePsr4[namespace]
+    if (undefined === overrideDir) {
+      continue
+    }
+    const from = normalizeOverlayRelativeDir(overrideDir)
+    const to = normalizeOverlayRelativeDir(consumerDir)
+    if ("" === from || "" === to || from === to) {
+      continue
+    }
+    moves.set(from, to)
+  }
+  if (0 === moves.size) {
+    return hydratedSource
+  }
+
+  // Copy into the overlay staging root before moving directories so the caller's
+  // checkout is never restructured in place (the hydrated source may still be
+  // the original when it already carried a vendor/ directory).
+  let effectiveSource = hydratedSource
+  if (effectiveSource === originalSource) {
+    effectiveSource = join(stagingRoot, "reconciled-source")
+    await cp(originalSource, effectiveSource, { recursive: true })
+  }
+
+  for (const [from, to] of moves) {
+    const fromPath = join(effectiveSource, from)
+    const toPath = join(effectiveSource, to)
+    if (fromPath === toPath || !await pathIsDirectory(fromPath) || await pathExists(toPath)) {
+      continue
+    }
+    await mkdir(dirname(toPath), { recursive: true })
+    await rename(fromPath, toPath)
+  }
+  return effectiveSource
+}
+
+/** @return namespace-prefix -> normalized relative source dir, or undefined. */
+async function composerPackagePsr4FromInstalled(installedPath: string, packageName: string): Promise<Record<string, string> | undefined> {
+  try {
+    const pkg = composerInstalledPackageRecords(JSON.parse(await readFile(installedPath, "utf8"))).find((candidate) => candidate.name === packageName)
+    return pkg ? psr4SingleDirMap((pkg as ComposerInstalledPackage).autoload?.["psr-4"]) : undefined
+  } catch {
+    return undefined
+  }
+}
+
+async function composerPackagePsr4FromComposerJson(composerPath: string): Promise<Record<string, string> | undefined> {
+  try {
+    const composer = JSON.parse(await readFile(composerPath, "utf8")) as { autoload?: { "psr-4"?: Record<string, string | string[]> } }
+    return psr4SingleDirMap(composer.autoload?.["psr-4"])
+  } catch {
+    return undefined
+  }
+}
+
+/** Keep only single-directory PSR-4 mappings; multi-dir prefixes are ambiguous to relocate. */
+function psr4SingleDirMap(psr4: Record<string, string | string[]> | undefined): Record<string, string> | undefined {
+  if (!psr4) {
+    return undefined
+  }
+  const map: Record<string, string> = {}
+  for (const [namespace, dirs] of Object.entries(psr4)) {
+    const list = Array.isArray(dirs) ? dirs : [dirs]
+    if (1 === list.length && "string" === typeof list[0]) {
+      map[namespace] = list[0]
+    }
+  }
+  return Object.keys(map).length > 0 ? map : undefined
+}
+
+function normalizeOverlayRelativeDir(dir: string): string {
+  const normalized = dir.replace(/\\/g, "/").replace(/^\.\//, "").replace(/^\/+/, "").replace(/\/+$/, "")
+  return normalized.includes("..") ? "" : normalized
+}
+
+async function pathExists(path: string): Promise<boolean> {
+  try {
+    await stat(path)
+    return true
+  } catch {
+    return false
+  }
+}
+
 /**
  * Capture the clean checkout commit before Composer staging so runtime
  * provenance remains tied to the source revision rather than its staged path.
diff --git a/scripts/composer-package-overlay-autoload-layout-smoke.ts b/scripts/composer-package-overlay-autoload-layout-smoke.ts
new file mode 100644
index 000000000..0aeeb66e3
--- /dev/null
+++ b/scripts/composer-package-overlay-autoload-layout-smoke.ts
@@ -0,0 +1,86 @@
+import assert from "node:assert/strict"
+import { mkdir, mkdtemp, readFile, rm, stat, writeFile } from "node:fs/promises"
+import { tmpdir } from "node:os"
+import { join } from "node:path"
+import { prepareRecipeDependencyOverlays } from "../packages/cli/src/recipe-sources.js"
+import type { PreparedExtraPlugin } from "../packages/cli/src/recipe-sources.js"
+
+// Proves the dependency overlay reconciles its on-disk PSR-4 layout to the
+// path the consumer's committed autoloader resolves. A repo published as
+// `src/` but consumed as `php-transformer/src/` (Blocks Engine's transformer,
+// mounted into Static Site Importer) would otherwise land where the consumer
+// autoloader never looks, so the override is silently ignored and the pinned
+// released version keeps running.
+
+const root = await mkdtemp(join(tmpdir(), "wp-codebox-overlay-autoload-layout-"))
+
+async function exists(path: string): Promise<boolean> {
+  try {
+    await stat(path)
+    return true
+  } catch {
+    return false
+  }
+}
+
+// Override checkout ships its class under the package-canonical `src/` layout,
+// with a prebuilt vendor/ so no Composer hydration is needed.
+const overrideSource = join(root, "blocks-engine-php-transformer")
+await mkdir(join(overrideSource, "src", "ArtifactCompiler"), { recursive: true })
+await writeFile(join(overrideSource, "src", "ArtifactCompiler", "ArtifactCompiler.php"), "<?php\nnamespace Automattic\\BlocksEngine\\PhpTransformer\\ArtifactCompiler;\nfinal class ArtifactCompiler {}\n")
+await writeFile(join(overrideSource, "composer.json"), JSON.stringify({
+  name: "automattic/blocks-engine-php-transformer",
+  autoload: { "psr-4": { "Automattic\\BlocksEngine\\PhpTransformer\\": "src/" } },
+}, null, 2))
+await mkdir(join(overrideSource, "vendor", "composer"), { recursive: true })
+await writeFile(join(overrideSource, "vendor", "composer", "installed.json"), JSON.stringify({ packages: [
+  { name: "automattic/blocks-engine-php-transformer", autoload: { "psr-4": { "Automattic\\BlocksEngine\\PhpTransformer\\": "src/" } } },
+] }, null, 2))
+
+// Consumer records the same package under the repo-relative `php-transformer/src/`
+// layout its release zip extracts to.
+const consumerSource = join(root, "consumer-plugin")
+await mkdir(join(consumerSource, "vendor", "composer"), { recursive: true })
+await writeFile(join(consumerSource, "vendor", "composer", "installed.json"), JSON.stringify({ packages: [
+  { name: "automattic/blocks-engine-php-transformer", version: "0.4.4", autoload: { "psr-4": { "Automattic\\BlocksEngine\\PhpTransformer\\": "php-transformer/src/" } } },
+] }, null, 2))
+
+const consumers: PreparedExtraPlugin[] = [{
+  source: consumerSource,
+  slug: "consumer-plugin",
+  target: "/wordpress/wp-content/plugins/consumer-plugin",
+  pluginFile: "consumer-plugin.php",
+  activate: true,
+  loadAs: "plugin",
+  cleanupPaths: [],
+  provenance: { kind: "local", original: consumerSource },
+}]
+
+const dependencyOverlays = await prepareRecipeDependencyOverlays({
+  inputs: {
+    dependency_overlays: [{
+      kind: "composer-package",
+      package: "automattic/blocks-engine-php-transformer",
+      source: overrideSource,
+      consumer: "consumer-plugin",
+    }],
+  },
+}, root, consumers)
+
+try {
+  assert.equal(dependencyOverlays.length, 1)
+  const staged = dependencyOverlays[0].source
+  // The class must be relocated to the consumer's recorded PSR-4 path so the
+  // consumer autoloader resolves it after the vendor-path mount.
+  assert.equal(await exists(join(staged, "php-transformer", "src", "ArtifactCompiler", "ArtifactCompiler.php")), true, "override class relocated to consumer PSR-4 layout")
+  assert.equal(await exists(join(staged, "src", "ArtifactCompiler", "ArtifactCompiler.php")), false, "override source layout no longer shadows the consumer path")
+  assert.equal(dependencyOverlays[0].target, "/wordpress/wp-content/plugins/consumer-plugin/vendor/automattic/blocks-engine-php-transformer")
+  // The override checkout itself is never mutated.
+  assert.equal(await exists(join(overrideSource, "php-transformer")), false, "override checkout is not restructured in place")
+  assert.equal(await exists(join(overrideSource, "src", "ArtifactCompiler", "ArtifactCompiler.php")), true, "override checkout keeps its own layout")
+} finally {
+  await Promise.all([...dependencyOverlays, ...consumers].flatMap((overlay) => overlay.cleanupPaths).map((path) => rm(path, { recursive: true, force: true })))
+  await rm(root, { recursive: true, force: true })
+}
+
+console.log("composer-package-overlay-autoload-layout-smoke: ok")
diff --git a/scripts/smoke-manifest.ts b/scripts/smoke-manifest.ts
index a72ca5bb4..b6c4088c5 100644
--- a/scripts/smoke-manifest.ts
+++ b/scripts/smoke-manifest.ts
@@ -122,6 +122,7 @@ export const smokeGroups = {
       npmScript("test:runtime-php-snippets"),
       npmScript("test:php-runtime-provider-registry"),
       tsxSmoke("composer-backed-source-hydration-smoke"),
+      tsxSmoke("composer-package-overlay-autoload-layout-smoke"),
       tsxSmoke("recipe-run-composer-autoload-extra-plugin-smoke"),
       tsxSmoke("runtime-component-lifecycle-replay-smoke"),
     ],