diff --git a/cli/args/mod.rs b/cli/args/mod.rs
index 3ff2a427fbf4d4..2ae7098da5ab44 100644
--- a/cli/args/mod.rs
+++ b/cli/args/mod.rs
@@ -1144,10 +1144,6 @@ impl CliOptions {
           DenoSubcommand::Run(run_flags) => {
             if run_flags.is_stdin() {
               resolve_url_or_path("./$deno$stdin.ts", self.initial_cwd())?
-            } else if NpmPackageReqReference::from_str(&run_flags.script)
-              .is_ok()
-            {
-              ModuleSpecifier::parse(&run_flags.script)?
             } else {
               resolve_url_or_path(&run_flags.script, self.initial_cwd())?
             }
diff --git a/cli/graph_util.rs b/cli/graph_util.rs
index f7194ac11b6e38..e2f6246e740c04 100644
--- a/cli/graph_util.rs
+++ b/cli/graph_util.rs
@@ -21,6 +21,7 @@ use crate::tools::check::TypeChecker;
 use crate::util::file_watcher::WatcherCommunicator;
 use crate::util::fs::canonicalize_path;
 use deno_config::workspace::JsrPackageConfig;
+use deno_core::anyhow::bail;
 use deno_graph::source::LoaderChecksum;
 use deno_graph::FillFromLockfileOptions;
 use deno_graph::JsrLoadError;
@@ -593,6 +594,12 @@ impl ModuleGraphBuilder {
     let initial_package_deps_len = graph.packages.package_deps_sum();
     let initial_package_mappings_len = graph.packages.mappings().len();
 
+    if roots.iter().any(|r| r.scheme() == "npm")
+      && self.npm_resolver.as_byonm().is_some()
+    {
+      bail!("Resolving npm specifier entrypoints this way is currently not supported with \"nodeModules\": \"manual\". In the meantime, try with --node-modules-dir=auto instead");
+    }
+
     graph.build(roots, loader, options).await;
 
     let has_redirects_changed = graph.redirects.len() != initial_redirects_len;
diff --git a/tests/specs/info/byonm/__test__.jsonc b/tests/specs/info/byonm/__test__.jsonc
new file mode 100644
index 00000000000000..6c9ba7dadaee25
--- /dev/null
+++ b/tests/specs/info/byonm/__test__.jsonc
@@ -0,0 +1,11 @@
+{
+  "tempDir": true,
+  "steps": [{
+    "args": "install",
+    "output": "[WILDCARD]"
+  }, {
+    "args": "info npm:@denotest/add",
+    "output": "info.out",
+    "exitCode": 1
+  }]
+}
diff --git a/tests/specs/info/byonm/deno.json b/tests/specs/info/byonm/deno.json
new file mode 100644
index 00000000000000..4b88c71fbb3f87
--- /dev/null
+++ b/tests/specs/info/byonm/deno.json
@@ -0,0 +1,6 @@
+{
+  "nodeModulesDir": "manual",
+  "imports": {
+    "chalk": "npm:@denotest/add"
+  }
+}
diff --git a/tests/specs/info/byonm/info.out b/tests/specs/info/byonm/info.out
new file mode 100644
index 00000000000000..4e6f11a88ff29d
--- /dev/null
+++ b/tests/specs/info/byonm/info.out
@@ -0,0 +1 @@
+error: Resolving npm specifier entrypoints this way is currently not supported with "nodeModules": "manual". In the meantime, try with --node-modules-dir=auto instead
diff --git a/tests/specs/info/byonm/package.json b/tests/specs/info/byonm/package.json
new file mode 100644
index 00000000000000..15a786ad71fa22
--- /dev/null
+++ b/tests/specs/info/byonm/package.json
@@ -0,0 +1,5 @@
+{
+  "dependencies": {
+    "@denotest/add": "*"
+  }
+}