diff --git a/news/changelog-1.11.md b/news/changelog-1.11.md
index 1b80a1502a7..1dfd7680c96 100644
--- a/news/changelog-1.11.md
+++ b/news/changelog-1.11.md
@@ -208,3 +208,4 @@ All changes included in 1.11:
 - ([#15157](https://github.com/quarto-dev/quarto-cli/issues/15157)): Fix `quarto preview` and other commands sometimes starting a local server on port 4190, which browsers refuse to connect to.
 - ([#15180](https://github.com/quarto-dev/quarto-cli/pull/15180)): Fix older Quarto versions failing to render with `RangeError: could not deserialize value` once a Quarto built on a newer Deno has used the same cache. Also fix a project cache that already has entries failing to clear with `Path must be a string`.
 - ([#15198](https://github.com/quarto-dev/quarto-cli/issues/15198)): Fix `quarto add`, `quarto use template`, `quarto use brand` and `quarto install tinytex` failing to unzip on Windows when a Group Policy blocks running `.bat` files from the temporary folder, and when a path contains an apostrophe.
+- ([#15227](https://github.com/quarto-dev/quarto-cli/pull/15227)): Fix TypeScript scripts run by Quarto, such as `quarto run` scripts, project pre- and post-render scripts and Jupyter filters, losing their downloaded npm packages on Windows, which made them fail when run offline (regression introduced in v1.9).
diff --git a/src/core/run/deno.ts b/src/core/run/deno.ts
index add8c21b782..9303e89635e 100644
--- a/src/core/run/deno.ts
+++ b/src/core/run/deno.ts
@@ -81,10 +81,16 @@ function directoryListing(path: string): Set<string> {
   );
 }
 
-function directoryListingsMatch(path1: string, path2: string): boolean {
+// Deno may leave these in the seed and delete them from the user copy on a clean close
+const kSqliteSidecar = /_cache_v2-(shm|wal|journal)$/;
+
+export function directoryListingsMatch(path1: string, path2: string): boolean {
   const listing1 = directoryListing(path1),
     listing2 = directoryListing(path2);
   for (const path of listing1) {
+    if (kSqliteSidecar.test(path)) {
+      continue;
+    }
     if (!listing2.has(path)) {
       return false;
     }
diff --git a/tests/unit/core/deno-std-cache.test.ts b/tests/unit/core/deno-std-cache.test.ts
new file mode 100644
index 00000000000..4b0fca45572
--- /dev/null
+++ b/tests/unit/core/deno-std-cache.test.ts
@@ -0,0 +1,110 @@
+/*
+ * deno-std-cache.test.ts
+ *
+ * Copyright (C) 2026 Posit Software, PBC
+ */
+
+import { ensureDirSync } from "../../../src/deno_ral/fs.ts";
+import { dirname, join } from "../../../src/deno_ral/path.ts";
+import { directoryListingsMatch } from "../../../src/core/run/deno.ts";
+import { unitTest } from "../../test.ts";
+import { assertEquals } from "../../asserts.ts";
+import { withTempDir } from "../../utils.ts";
+
+const touch = (root: string, rel: string) => {
+  const file = join(root, rel);
+  ensureDirSync(dirname(file));
+  Deno.writeTextFileSync(file, "");
+};
+
+const populate = (root: string, rels: string[]) => {
+  ensureDirSync(root);
+  rels.forEach((rel) => touch(root, rel));
+};
+
+const compare = (seedFiles: string[], userFiles: string[]) =>
+  withTempDir((dir) => {
+    const seed = join(dir, "seed");
+    const user = join(dir, "user");
+    populate(seed, seedFiles);
+    populate(user, userFiles);
+    return directoryListingsMatch(seed, user);
+  });
+
+// Deno can exit `deno cache` without closing its SQLite cache databases, so the
+// bundled seed may hold -shm/-wal files that a later clean close deletes from
+// the user copy. Those must not count as a missing seed file.
+unitTest(
+  "directoryListingsMatch - ignores SQLite cache sidecars missing from the user copy",
+  async () => {
+    const result = await compare(
+      [
+        "cache/dep_analysis_cache_v2",
+        "cache/dep_analysis_cache_v2-shm",
+        "cache/dep_analysis_cache_v2-wal",
+        "cache/v8_code_cache_v2",
+        "cache/v8_code_cache_v2-wal",
+        "cache/npm/x/y.json",
+      ],
+      [
+        "cache/dep_analysis_cache_v2",
+        "cache/v8_code_cache_v2",
+        "cache/npm/x/y.json",
+      ],
+    );
+    assertEquals(result, true);
+  },
+);
+
+unitTest(
+  "directoryListingsMatch - reports a missing ordinary file",
+  async () => {
+    const result = await compare(
+      [
+        "cache/dep_analysis_cache_v2",
+        "cache/dep_analysis_cache_v2-shm",
+        "cache/dep_analysis_cache_v2-wal",
+        "cache/v8_code_cache_v2",
+        "cache/v8_code_cache_v2-wal",
+        "cache/npm/x/y.json",
+        "cache/npm/x/z.json",
+      ],
+      [
+        "cache/dep_analysis_cache_v2",
+        "cache/v8_code_cache_v2",
+        "cache/npm/x/z.json",
+      ],
+    );
+    assertEquals(result, false);
+  },
+);
+
+unitTest(
+  "directoryListingsMatch - does not ignore package files with sidecar-like names",
+  async () => {
+    const result = await compare(
+      [
+        "cache/dep_analysis_cache_v2",
+        "cache/npm/x/y.json",
+        "cache/npm/x/foo-wal",
+      ],
+      ["cache/dep_analysis_cache_v2", "cache/npm/x/y.json"],
+    );
+    assertEquals(result, false);
+  },
+);
+
+unitTest(
+  "directoryListingsMatch - reports a missing cache database",
+  async () => {
+    const result = await compare(
+      [
+        "cache/dep_analysis_cache_v2",
+        "cache/dep_analysis_cache_v2-wal",
+        "cache/npm/x/y.json",
+      ],
+      ["cache/npm/x/y.json"],
+    );
+    assertEquals(result, false);
+  },
+);
diff --git a/tools/runtime-boundary-baseline.json b/tools/runtime-boundary-baseline.json
index 0607c709f10..729d34db7b6 100644
--- a/tools/runtime-boundary-baseline.json
+++ b/tools/runtime-boundary-baseline.json
@@ -16,7 +16,7 @@
     "stdImportFiles": 3
   },
   "tests": {
-    "denoCalls": 874,
+    "denoCalls": 875,
     "stdImportFiles": 176
   }
 }