diff --git a/cli/graph_util.rs b/cli/graph_util.rs
index 53d06071c85927..90c4f8b3889a4c 100644
--- a/cli/graph_util.rs
+++ b/cli/graph_util.rs
@@ -296,6 +296,12 @@ impl ModuleGraphBuilder {
     loader: &mut dyn deno_graph::source::Loader,
     options: deno_graph::BuildOptions<'a>,
   ) -> Result<(), AnyError> {
+    // ensure an "npm install" is done if the user has explicitly
+    // opted into using a node_modules directory
+    if self.options.node_modules_dir_enablement() == Some(true) {
+      self.resolver.force_top_level_package_json_install().await?;
+    }
+
     graph.build(roots, loader, options).await;
 
     // ensure that the top level package.json is installed if a
diff --git a/cli/resolver.rs b/cli/resolver.rs
index 7f49116f46f607..6fa8eaabef234d 100644
--- a/cli/resolver.rs
+++ b/cli/resolver.rs
@@ -182,14 +182,20 @@ impl CliGraphResolver {
     self
   }
 
+  pub async fn force_top_level_package_json_install(
+    &self,
+  ) -> Result<(), AnyError> {
+    self
+      .package_json_deps_installer
+      .ensure_top_level_install()
+      .await
+  }
+
   pub async fn top_level_package_json_install_if_necessary(
     &self,
   ) -> Result<(), AnyError> {
     if self.found_package_json_dep_flag.is_raised() {
-      self
-        .package_json_deps_installer
-        .ensure_top_level_install()
-        .await?;
+      self.force_top_level_package_json_install().await?;
     }
     Ok(())
   }
diff --git a/cli/tests/integration/npm_tests.rs b/cli/tests/integration/npm_tests.rs
index 73ac029df34c1b..bd19ed26f9a2a2 100644
--- a/cli/tests/integration/npm_tests.rs
+++ b/cli/tests/integration/npm_tests.rs
@@ -1,6 +1,7 @@
 // Copyright 2018-2023 the Deno authors. All rights reserved. MIT license.
 
 use deno_core::serde_json;
+use deno_core::serde_json::json;
 use deno_core::serde_json::Value;
 use pretty_assertions::assert_eq;
 use std::process::Stdio;
@@ -1924,3 +1925,73 @@ pub fn node_modules_dir_config_file() {
     .run();
   assert!(node_modules_dir.exists());
 }
+
+#[test]
+fn top_level_install_package_json_explicit_opt_in() {
+  let test_context = TestContextBuilder::for_npm().use_temp_cwd().build();
+  let temp_dir = test_context.temp_dir();
+  let node_modules_dir = temp_dir.path().join("node_modules");
+  let rm_created_files = || {
+    std::fs::remove_dir_all(&node_modules_dir).unwrap();
+    std::fs::remove_file(temp_dir.path().join("deno.lock")).unwrap();
+  };
+
+  // when the node_modules_dir is explicitly opted into, we should always
+  // ensure a top level package.json install occurs
+  temp_dir.write("deno.json", "{ \"nodeModulesDir\": true }");
+  temp_dir.write(
+    "package.json",
+    "{ \"dependencies\": { \"@denotest/esm-basic\": \"1.0\" }}",
+  );
+
+  temp_dir.write("main.ts", "console.log(5);");
+  let output = test_context.new_command().args("cache main.ts").run();
+  output.assert_matches_text(
+    concat!(
+      "Download http://localhost:4545/npm/registry/@denotest/esm-basic\n",
+      "Download http://localhost:4545/npm/registry/@denotest/esm-basic/1.0.0.tgz\n",
+      "Initialize @denotest/esm-basic@1.0.0\n",
+    )
+  );
+
+  rm_created_files();
+  let output = test_context
+    .new_command()
+    .args_vec(["eval", "console.log(5)"])
+    .run();
+  output.assert_matches_text(concat!(
+    "Initialize @denotest/esm-basic@1.0.0\n",
+    "5\n"
+  ));
+
+  rm_created_files();
+  let output = test_context
+    .new_command()
+    .args("run -")
+    .stdin("console.log(5)")
+    .run();
+  output.assert_matches_text(concat!(
+    "Initialize @denotest/esm-basic@1.0.0\n",
+    "5\n"
+  ));
+
+  // now ensure this is cached in the lsp
+  rm_created_files();
+  let mut client = test_context.new_lsp_command().build();
+  client.initialize_default();
+  let file_uri = temp_dir.uri().join("file.ts").unwrap();
+  client.did_open(json!({
+    "textDocument": {
+      "uri": file_uri,
+      "languageId": "typescript",
+      "version": 1,
+      "text": "",
+    }
+  }));
+  client.write_request(
+    "deno/cache",
+    json!({ "referrer": { "uri": file_uri }, "uris": [] }),
+  );
+
+  assert!(node_modules_dir.join("@denotest").exists());
+}
diff --git a/cli/tools/run.rs b/cli/tools/run.rs
index 99312d5b90d677..4805ea704d8b7d 100644
--- a/cli/tools/run.rs
+++ b/cli/tools/run.rs
@@ -47,6 +47,8 @@ To grant permissions, set them before the script argument. For example:
 
   let main_module = cli_options.resolve_main_module()?;
 
+  maybe_npm_install(&factory).await?;
+
   let permissions = PermissionsContainer::new(Permissions::from_options(
     &cli_options.permissions_options(),
   )?);
@@ -63,9 +65,11 @@ pub async fn run_from_stdin(flags: Flags) -> Result<i32, AnyError> {
   let factory = CliFactory::from_flags(flags).await?;
   let cli_options = factory.cli_options();
   let main_module = cli_options.resolve_main_module()?;
+
+  maybe_npm_install(&factory).await?;
+
   let file_fetcher = factory.file_fetcher()?;
   let worker_factory = factory.create_cli_main_worker_factory().await?;
-
   let permissions = PermissionsContainer::new(Permissions::from_options(
     &cli_options.permissions_options(),
   )?);
@@ -103,9 +107,11 @@ async fn run_with_watch(flags: Flags) -> Result<i32, AnyError> {
   let cli_options = factory.cli_options();
   let clear_screen = !cli_options.no_clear_screen();
   let main_module = cli_options.resolve_main_module()?;
+
+  maybe_npm_install(&factory).await?;
+
   let create_cli_main_worker_factory =
     factory.create_cli_main_worker_factory_func().await?;
-
   let operation = |main_module: ModuleSpecifier| {
     file_watcher.reset();
     let permissions = PermissionsContainer::new(Permissions::from_options(
@@ -144,12 +150,10 @@ pub async fn eval_command(
   let factory = CliFactory::from_flags(flags).await?;
   let cli_options = factory.cli_options();
   let file_fetcher = factory.file_fetcher()?;
-  let main_worker_factory = factory.create_cli_main_worker_factory().await?;
-
   let main_module = cli_options.resolve_main_module()?;
-  let permissions = PermissionsContainer::new(Permissions::from_options(
-    &cli_options.permissions_options(),
-  )?);
+
+  maybe_npm_install(&factory).await?;
+
   // Create a dummy source file.
   let source_code = if eval_flags.print {
     format!("console.log({})", eval_flags.code)
@@ -171,9 +175,26 @@ pub async fn eval_command(
   // to allow module access by TS compiler.
   file_fetcher.insert_cached(file);
 
-  let mut worker = main_worker_factory
+  let permissions = PermissionsContainer::new(Permissions::from_options(
+    &cli_options.permissions_options(),
+  )?);
+  let worker_factory = factory.create_cli_main_worker_factory().await?;
+  let mut worker = worker_factory
     .create_main_worker(main_module, permissions)
     .await?;
   let exit_code = worker.run().await?;
   Ok(exit_code)
 }
+
+async fn maybe_npm_install(factory: &CliFactory) -> Result<(), AnyError> {
+  // ensure an "npm install" is done if the user has explicitly
+  // opted into using a node_modules directory
+  if factory.cli_options().node_modules_dir_enablement() == Some(true) {
+    factory
+      .package_json_deps_installer()
+      .await?
+      .ensure_top_level_install()
+      .await?;
+  }
+  Ok(())
+}