diff --git a/cli/resolver.rs b/cli/resolver.rs
index 5b657b8953..07cb6931df 100644
--- a/cli/resolver.rs
+++ b/cli/resolver.rs
@@ -707,7 +707,14 @@ impl Resolver for CliGraphResolver {
             .resolve_if_for_npm_pkg(raw_specifier, referrer, to_node_mode(mode))
             .map_err(ResolveError::Other)?;
           if let Some(res) = maybe_resolution {
-            return Ok(res.into_url());
+            match res {
+              NodeResolution::Esm(url) | NodeResolution::CommonJs(url) => {
+                return Ok(url)
+              }
+              NodeResolution::BuiltIn(_) => {
+                // don't resolve bare specifiers for built-in modules via node resolution
+              }
+            }
           }
         }
 
diff --git a/tests/integration/run_tests.rs b/tests/integration/run_tests.rs
index 301283e85b..ef688517f9 100644
--- a/tests/integration/run_tests.rs
+++ b/tests/integration/run_tests.rs
@@ -4605,64 +4605,6 @@ fn permission_prompt_escapes_ansi_codes_and_control_chars() {
   }
 }
 
-itest!(node_builtin_modules_ts {
-  args: "run --quiet --allow-read run/node_builtin_modules/mod.ts hello there",
-  output: "run/node_builtin_modules/mod.ts.out",
-  envs: env_vars_for_npm_tests(),
-  exit_code: 0,
-});
-
-itest!(node_builtin_modules_js {
-  args: "run --quiet --allow-read run/node_builtin_modules/mod.js hello there",
-  output: "run/node_builtin_modules/mod.js.out",
-  envs: env_vars_for_npm_tests(),
-  exit_code: 0,
-});
-
-itest!(node_prefix_missing {
-  args: "run --quiet run/node_prefix_missing/main.ts",
-  output: "run/node_prefix_missing/main.ts.out",
-  envs: env_vars_for_npm_tests(),
-  exit_code: 1,
-});
-
-itest!(node_prefix_missing_unstable_bare_node_builtins_enbaled {
-  args: "run --unstable-bare-node-builtins run/node_prefix_missing/main.ts",
-  output: "run/node_prefix_missing/feature_enabled.out",
-  envs: env_vars_for_npm_tests(),
-  exit_code: 0,
-});
-
-itest!(
-  node_prefix_missing_unstable_bare_node_builtins_enbaled_by_env {
-    args: "run run/node_prefix_missing/main.ts",
-    output: "run/node_prefix_missing/feature_enabled.out",
-    envs: [
-      env_vars_for_npm_tests(),
-      vec![(
-        "DENO_UNSTABLE_BARE_NODE_BUILTINS".to_string(),
-        "1".to_string()
-      )]
-    ]
-    .concat(),
-    exit_code: 0,
-  }
-);
-
-itest!(node_prefix_missing_unstable_bare_node_builtins_enbaled_by_config {
-  args: "run --config=run/node_prefix_missing/config.json run/node_prefix_missing/main.ts",
-  output: "run/node_prefix_missing/feature_enabled.out",
-  envs: env_vars_for_npm_tests(),
-  exit_code: 0,
-});
-
-itest!(node_prefix_missing_unstable_bare_node_builtins_enbaled_with_import_map {
-  args: "run --unstable-bare-node-builtins --import-map run/node_prefix_missing/import_map.json run/node_prefix_missing/main.ts",
-  output: "run/node_prefix_missing/feature_enabled.out",
-  envs: env_vars_for_npm_tests(),
-  exit_code: 0,
-});
-
 itest!(dynamic_import_syntax_error {
   args: "run -A run/dynamic_import_syntax_error.js",
   output: "run/dynamic_import_syntax_error.js.out",
diff --git a/tests/specs/run/node_builtin_modules/__test__.jsonc b/tests/specs/run/node_builtin_modules/__test__.jsonc
new file mode 100644
index 0000000000..f3d637ac61
--- /dev/null
+++ b/tests/specs/run/node_builtin_modules/__test__.jsonc
@@ -0,0 +1,12 @@
+{
+  "tests": {
+    "ts": {
+      "args": "run --quiet --allow-read mod.ts hello there",
+      "output": "mod.ts.out"
+    },
+    "js": {
+      "args": "run --quiet --allow-read mod.js hello there",
+      "output": "mod.js.out"
+    }
+  }
+}
diff --git a/tests/testdata/run/node_builtin_modules/mod.js b/tests/specs/run/node_builtin_modules/mod.js
similarity index 100%
rename from tests/testdata/run/node_builtin_modules/mod.js
rename to tests/specs/run/node_builtin_modules/mod.js
diff --git a/tests/testdata/run/node_builtin_modules/mod.js.out b/tests/specs/run/node_builtin_modules/mod.js.out
similarity index 100%
rename from tests/testdata/run/node_builtin_modules/mod.js.out
rename to tests/specs/run/node_builtin_modules/mod.js.out
diff --git a/tests/testdata/run/node_builtin_modules/mod.ts b/tests/specs/run/node_builtin_modules/mod.ts
similarity index 100%
rename from tests/testdata/run/node_builtin_modules/mod.ts
rename to tests/specs/run/node_builtin_modules/mod.ts
diff --git a/tests/testdata/run/node_builtin_modules/mod.ts.out b/tests/specs/run/node_builtin_modules/mod.ts.out
similarity index 100%
rename from tests/testdata/run/node_builtin_modules/mod.ts.out
rename to tests/specs/run/node_builtin_modules/mod.ts.out
diff --git a/tests/specs/run/node_prefix_missing/__test__.jsonc b/tests/specs/run/node_prefix_missing/__test__.jsonc
new file mode 100644
index 0000000000..305020ed97
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/__test__.jsonc
@@ -0,0 +1,35 @@
+{
+  "tests": {
+    "basic": {
+      "args": "run --quiet main.ts",
+      "output": "main.ts.out",
+      "exitCode": 1
+    },
+    "unstable_bare_node_builtins_enabled": {
+      "args": "run --unstable-bare-node-builtins main.ts",
+      "output": "feature_enabled.out"
+    },
+    "unstable_bare_node_builtins_enbaled_by_env": {
+      "args": "run main.ts",
+      "envs": {
+        "DENO_UNSTABLE_BARE_NODE_BUILTINS": "1"
+      },
+      "output": "feature_enabled.out"
+    },
+    "enabled_by_config": {
+      "args": "run --config=config.json main.ts",
+      "output": "feature_enabled.out"
+    },
+    "byonm_missing": {
+      "cwd": "byonm",
+      "exitCode": 1,
+      "args": "run missing.ts",
+      "output": "byonm/missing.out"
+    },
+    "byonm_has": {
+      "cwd": "byonm",
+      "args": "run has.ts",
+      "output": "byonm/has.out"
+    }
+  }
+}
diff --git a/tests/specs/run/node_prefix_missing/byonm/has.out b/tests/specs/run/node_prefix_missing/byonm/has.out
new file mode 100644
index 0000000000..e223dcff58
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/byonm/has.out
@@ -0,0 +1 @@
+[Function: writeFile]
diff --git a/tests/specs/run/node_prefix_missing/byonm/has.ts b/tests/specs/run/node_prefix_missing/byonm/has.ts
new file mode 100644
index 0000000000..a52c1e3f0d
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/byonm/has.ts
@@ -0,0 +1,3 @@
+import fs from "node:fs";
+
+console.log(fs.writeFile);
diff --git a/tests/specs/run/node_prefix_missing/byonm/missing.out b/tests/specs/run/node_prefix_missing/byonm/missing.out
new file mode 100644
index 0000000000..4129e79a51
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/byonm/missing.out
@@ -0,0 +1,3 @@
+error: Relative import path "fs" not prefixed with / or ./ or ../
+  hint: If you want to use a built-in Node module, add a "node:" prefix (ex. "node:fs").
+    at file:///[WILDLINE]/missing.ts:1:16
diff --git a/tests/testdata/run/node_prefix_missing/main.ts b/tests/specs/run/node_prefix_missing/byonm/missing.ts
similarity index 100%
rename from tests/testdata/run/node_prefix_missing/main.ts
rename to tests/specs/run/node_prefix_missing/byonm/missing.ts
diff --git a/tests/specs/run/node_prefix_missing/byonm/package.json b/tests/specs/run/node_prefix_missing/byonm/package.json
new file mode 100644
index 0000000000..2c63c08510
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/byonm/package.json
@@ -0,0 +1,2 @@
+{
+}
diff --git a/tests/specs/run/node_prefix_missing/config.json b/tests/specs/run/node_prefix_missing/config.json
new file mode 100644
index 0000000000..72f40aaf36
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/config.json
@@ -0,0 +1,3 @@
+{
+  "unstable": ["bare-node-builtins"]
+}
diff --git a/tests/specs/run/node_prefix_missing/feature_enabled.out b/tests/specs/run/node_prefix_missing/feature_enabled.out
new file mode 100644
index 0000000000..3eff4bc324
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/feature_enabled.out
@@ -0,0 +1,2 @@
+[WILDCARD]Warning Resolving "fs" as "node:fs" at file:///[WILDCARD]/main.ts:1:16. If you want to use a built-in Node module, add a "node:" prefix.
+[Function: writeFile]
diff --git a/tests/specs/run/node_prefix_missing/main.ts b/tests/specs/run/node_prefix_missing/main.ts
new file mode 100644
index 0000000000..c5c1885a2f
--- /dev/null
+++ b/tests/specs/run/node_prefix_missing/main.ts
@@ -0,0 +1,3 @@
+import fs from "fs";
+
+console.log(fs.writeFile);
diff --git a/tests/testdata/run/node_prefix_missing/main.ts.out b/tests/specs/run/node_prefix_missing/main.ts.out
similarity index 100%
rename from tests/testdata/run/node_prefix_missing/main.ts.out
rename to tests/specs/run/node_prefix_missing/main.ts.out
diff --git a/tests/testdata/run/node_prefix_missing/config.json b/tests/testdata/run/node_prefix_missing/config.json
deleted file mode 100644
index 67480c3d48..0000000000
--- a/tests/testdata/run/node_prefix_missing/config.json
+++ /dev/null
@@ -1 +0,0 @@
-{ "unstable": ["bare-node-builtins"] }
diff --git a/tests/testdata/run/node_prefix_missing/feature_enabled.out b/tests/testdata/run/node_prefix_missing/feature_enabled.out
deleted file mode 100644
index c577fa92cb..0000000000
--- a/tests/testdata/run/node_prefix_missing/feature_enabled.out
+++ /dev/null
@@ -1,2 +0,0 @@
-[WILDCARD]Warning Resolving "fs" as "node:fs" at file:///[WILDCARD]/tests/testdata/run/node_prefix_missing/main.ts:1:16. If you want to use a built-in Node module, add a "node:" prefix.
-[Function: writeFile]
diff --git a/tests/testdata/run/node_prefix_missing/import_map.json b/tests/testdata/run/node_prefix_missing/import_map.json
deleted file mode 100644
index 3add7d009c..0000000000
--- a/tests/testdata/run/node_prefix_missing/import_map.json
+++ /dev/null
@@ -1 +0,0 @@
-{ "imports": {} }
diff --git a/tools/lint.js b/tools/lint.js
index 74b2c28d31..db4b657af7 100755
--- a/tools/lint.js
+++ b/tools/lint.js
@@ -220,7 +220,7 @@ async function ensureNoNewITests() {
     "pm_tests.rs": 0,
     "publish_tests.rs": 0,
     "repl_tests.rs": 0,
-    "run_tests.rs": 347,
+    "run_tests.rs": 340,
     "shared_library_tests.rs": 0,
     "task_tests.rs": 30,
     "test_tests.rs": 74,