diff --git a/tests/specs/run/sourcemap_nonexistent_source/__test__.jsonc b/tests/specs/run/sourcemap_nonexistent_source/__test__.jsonc
index 8b18f886d9..711b238f7d 100644
--- a/tests/specs/run/sourcemap_nonexistent_source/__test__.jsonc
+++ b/tests/specs/run/sourcemap_nonexistent_source/__test__.jsonc
@@ -1,6 +1,14 @@
 {
-  "ignore": true,
-  "args": "run bundle.js",
-  "output": "bundle.js.out",
-  "exitCode": 1
+  "tests": {
+    "node_modules": {
+      "args": "run --allow-read node_modules.ts",
+      "output": "node_modules.out",
+      "exitCode": 1
+    },
+    "not_node_modules": {
+      "args": "run not_node_modules.js",
+      "output": "not_node_modules.out",
+      "exitCode": 1
+    }
+  }
 }
diff --git a/tests/specs/run/sourcemap_nonexistent_source/bundle.js.map b/tests/specs/run/sourcemap_nonexistent_source/bundle.js.map
deleted file mode 100644
index 915fc0c910..0000000000
--- a/tests/specs/run/sourcemap_nonexistent_source/bundle.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"bundle.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,2BAA2B;AAC3B,SAAS,UAAU;IACjB,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;AACxD,CAAC;AAED,UAAU,EAAE,CAAC"}
diff --git a/tests/specs/run/sourcemap_nonexistent_source/bundle.js.out b/tests/specs/run/sourcemap_nonexistent_source/bundle.js.out
deleted file mode 100644
index 31d7fd59f6..0000000000
--- a/tests/specs/run/sourcemap_nonexistent_source/bundle.js.out
+++ /dev/null
@@ -1,5 +0,0 @@
-error: Uncaught (in promise) Error: Test error from bundle with missing source
-  throw new Error("Test error from bundle with missing source");
-  ^
-    at throwError ([WILDCARD]bundle.js:3:3)
-    at [WILDCARD]bundle.js:6:14
diff --git a/tests/specs/run/sourcemap_nonexistent_source/deno.json b/tests/specs/run/sourcemap_nonexistent_source/deno.json
new file mode 100644
index 0000000000..fde86a1efb
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/deno.json
@@ -0,0 +1,3 @@
+{
+  "nodeModulesDir": "manual"
+}
diff --git a/tests/specs/run/sourcemap_nonexistent_source/node_modules.out b/tests/specs/run/sourcemap_nonexistent_source/node_modules.out
new file mode 100644
index 0000000000..ccc14495b5
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/node_modules.out
@@ -0,0 +1,3 @@
+error: Uncaught (in promise) Error: Test error from npm bundle with missing source
+    at throwError ([WILDCARD]node_modules/test-pkg/bundle.js:3:9)
+    at [WILDCARD]node_modules.ts:3:1
diff --git a/tests/specs/run/sourcemap_nonexistent_source/node_modules.ts b/tests/specs/run/sourcemap_nonexistent_source/node_modules.ts
new file mode 100644
index 0000000000..ef71087b30
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/node_modules.ts
@@ -0,0 +1,3 @@
+import { throwError } from "test-pkg";
+
+throwError();
diff --git a/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/bundle.js b/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/bundle.js
new file mode 100644
index 0000000000..e68cd1677d
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/bundle.js
@@ -0,0 +1,8 @@
+// Simulates an npm package bundle where source files don't exist
+function throwError() {
+  throw new Error("Test error from npm bundle with missing source");
+}
+
+module.exports = { throwError };
+
+//# sourceMappingURL=bundle.js.map
diff --git a/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/bundle.js.map b/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/bundle.js.map
new file mode 100644
index 0000000000..622a44b386
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/bundle.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"bundle.js","sourceRoot":"","sources":["src/index.ts"],"names":[],"mappings":"AAAA,2BAA2B;AAC3B,SAAS,UAAU;IACjB,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAC;AAChE,CAAC;AAED,OAAO,CAAC,OAAO,GAAG,EAAE,UAAU,EAAE,CAAC"}
diff --git a/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/package.json b/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/package.json
new file mode 100644
index 0000000000..f04f163917
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/node_modules/test-pkg/package.json
@@ -0,0 +1,5 @@
+{
+  "name": "test-pkg",
+  "version": "1.0.0",
+  "main": "bundle.js"
+}
diff --git a/tests/specs/run/sourcemap_nonexistent_source/bundle.js b/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.js
similarity index 79%
rename from tests/specs/run/sourcemap_nonexistent_source/bundle.js
rename to tests/specs/run/sourcemap_nonexistent_source/not_node_modules.js
index 3ab5990791..88fe0e8282 100644
--- a/tests/specs/run/sourcemap_nonexistent_source/bundle.js
+++ b/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.js
@@ -5,4 +5,4 @@ function throwError() {
 
 throwError();
 
-//# sourceMappingURL=bundle.js.map
+//# sourceMappingURL=not_node_modules.js.map
diff --git a/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.js.map b/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.js.map
new file mode 100644
index 0000000000..8a686adf27
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"not_node_modules.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,2BAA2B;AAC3B,SAAS,UAAU;IACjB,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;AACxD,CAAC;AAED,UAAU,EAAE,CAAC"}
diff --git a/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.out b/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.out
new file mode 100644
index 0000000000..86795f0b71
--- /dev/null
+++ b/tests/specs/run/sourcemap_nonexistent_source/not_node_modules.out
@@ -0,0 +1,3 @@
+error: Uncaught (in promise) Error: Test error from bundle with missing source
+    at throwError ([WILDCARD]src/index.ts:3:3)
+    at [WILDCARD]src/index.ts:6:14