diff --git a/.changeset/dev-runtime-nitro-prune-protection.md b/.changeset/dev-runtime-nitro-prune-protection.md
new file mode 100644
index 000000000..9ef72875a
--- /dev/null
+++ b/.changeset/dev-runtime-nitro-prune-protection.md
@@ -0,0 +1,5 @@
+---
+"eve": patch
+---
+
+Protect dev-runtime snapshots referenced by generated Nitro artifacts from stale snapshot pruning, so `eve dev` routes do not lose boot-time compiled-artifact imports after rebuild churn.
diff --git a/packages/eve/src/internal/nitro/dev-runtime-artifacts.integration.test.ts b/packages/eve/src/internal/nitro/dev-runtime-artifacts.integration.test.ts
index e1e96ce02..9f87bc317 100644
--- a/packages/eve/src/internal/nitro/dev-runtime-artifacts.integration.test.ts
+++ b/packages/eve/src/internal/nitro/dev-runtime-artifacts.integration.test.ts
@@ -384,6 +384,58 @@ describe("development runtime artifact snapshots", () => {
     expect(existsSync(staleSnapshotRoot)).toBe(false);
   });
 
+  it("preserves snapshots referenced by generated Nitro files", async () => {
+    const appRoot = await createScratchDirectory("eve-dev-runtime-artifacts-prune-nitro-");
+    const snapshotsRoot = join(appRoot, ".eve", "dev-runtime", "snapshots");
+    const activeSnapshotRoot = join(snapshotsRoot, "active");
+    const nitroReferencedSnapshotRoot = join(snapshotsRoot, "nitro-referenced");
+    const staleSnapshotRoot = join(snapshotsRoot, "stale");
+    const oldSnapshotTime = new Date(1_000);
+
+    for (const snapshotRoot of [
+      activeSnapshotRoot,
+      nitroReferencedSnapshotRoot,
+      staleSnapshotRoot,
+    ]) {
+      await mkdir(snapshotRoot, { recursive: true });
+      await writeFile(join(snapshotRoot, "marker.txt"), snapshotRoot);
+      await utimes(snapshotRoot, oldSnapshotTime, oldSnapshotTime);
+    }
+
+    await activateDevelopmentRuntimeArtifactsSnapshot({
+      appRoot,
+      snapshot: {
+        runtimeAppRoot: join(activeSnapshotRoot, "source", "app"),
+        snapshotRoot: activeSnapshotRoot,
+        snapshotSourceRoot: join(activeSnapshotRoot, "source"),
+      },
+    });
+    await mkdir(join(appRoot, ".eve", "nitro", "workflow"), { recursive: true });
+    await writeFile(
+      join(appRoot, ".eve", "nitro", "workflow", "steps.mjs"),
+      `import "${join(
+        nitroReferencedSnapshotRoot,
+        "source",
+        "app",
+        ".eve",
+        "compile",
+        "compiled-artifacts-bootstrap.mjs",
+      ).replaceAll("\\", "/")}";\n`,
+    );
+
+    await pruneDevelopmentRuntimeArtifactsSnapshots({
+      appRoot,
+      now: 1_000_000,
+      recentWindowMs: 0,
+      retainCount: 0,
+    });
+
+    await expect(readdir(snapshotsRoot)).resolves.toEqual(
+      expect.arrayContaining(["active", "nitro-referenced"]),
+    );
+    expect(existsSync(staleSnapshotRoot)).toBe(false);
+  });
+
   it("removes a partially staged snapshot when staging fails", async () => {
     const appRoot = await createScratchDirectory("eve-dev-runtime-artifacts-failed-stage-");
     const agentRoot = join(appRoot, "agent");
diff --git a/packages/eve/src/internal/nitro/dev-runtime-artifacts.ts b/packages/eve/src/internal/nitro/dev-runtime-artifacts.ts
index 88c896d65..da5d31ffa 100644
--- a/packages/eve/src/internal/nitro/dev-runtime-artifacts.ts
+++ b/packages/eve/src/internal/nitro/dev-runtime-artifacts.ts
@@ -11,7 +11,7 @@ const DEV_RUNTIME_ARTIFACTS_DIRECTORY = "dev-runtime";
 const DEV_RUNTIME_ARTIFACTS_POINTER_VERSION = 2;
 const DEV_RUNTIME_SNAPSHOT_RECENT_WINDOW_MS = 15 * 60 * 1000;
 const DEV_RUNTIME_SNAPSHOT_RETAIN_COUNT = 5;
-const DEV_RUNTIME_WORKFLOW_DATA_MAX_SCAN_BYTES = 1024 * 1024;
+const DEV_RUNTIME_PROTECTED_REFERENCE_MAX_SCAN_BYTES = 1024 * 1024;
 const TERMINAL_WORKFLOW_RUN_STATUSES = new Set(["completed", "failed", "cancelled", "canceled"]);
 
 interface DevelopmentRuntimeArtifactsPointerV1 {
@@ -184,7 +184,10 @@ export async function pruneDevelopmentRuntimeArtifactsSnapshots(input: {
   );
   const protectedPaths = [
     ...collectProtectedSnapshotPaths(pointer),
-    ...(await collectWorkflowDataSnapshotPaths({ appRoot: input.appRoot, snapshotsDirectory })),
+    ...(await collectProtectedReferenceSnapshotPaths({
+      appRoot: input.appRoot,
+      snapshotsDirectory,
+    })),
   ];
   const now = input.now ?? Date.now();
   const recentWindowMs = input.recentWindowMs ?? DEV_RUNTIME_SNAPSHOT_RECENT_WINDOW_MS;
@@ -297,18 +300,25 @@ function collectProtectedSnapshotPaths(
   return [pointer.runtimeAppRoot, pointer.snapshotRoot];
 }
 
-async function collectWorkflowDataSnapshotPaths(input: {
+async function collectProtectedReferenceSnapshotPaths(input: {
   readonly appRoot: string;
   readonly snapshotsDirectory: string;
 }): Promise<readonly string[]> {
-  const workflowDataDirectory = join(input.appRoot, ".workflow-data");
+  const referenceDirectories = [
+    join(input.appRoot, ".workflow-data"),
+    join(input.appRoot, ".eve", "nitro"),
+  ];
   const snapshotPaths = new Set<string>();
 
-  await collectSnapshotPathsFromDirectory({
-    directory: workflowDataDirectory,
-    snapshotPaths,
-    snapshotsDirectory: input.snapshotsDirectory,
-  });
+  await Promise.all(
+    referenceDirectories.map((directory) =>
+      collectSnapshotPathsFromDirectory({
+        directory,
+        snapshotPaths,
+        snapshotsDirectory: input.snapshotsDirectory,
+      }),
+    ),
+  );
 
   return [...snapshotPaths];
 }
@@ -348,8 +358,8 @@ async function collectSnapshotPathsFromDirectory(input: {
       }
 
       const fileStats = await stat(path);
-      // Local workflow run payloads are small; keep this best-effort scan cheap.
-      if (fileStats.size > DEV_RUNTIME_WORKFLOW_DATA_MAX_SCAN_BYTES) {
+      // Protected-reference files are small; keep this best-effort scan cheap.
+      if (fileStats.size > DEV_RUNTIME_PROTECTED_REFERENCE_MAX_SCAN_BYTES) {
         return;
       }