diff --git a/cli/lsp/config.rs b/cli/lsp/config.rs
index d204dce646..f9262d12e8 100644
--- a/cli/lsp/config.rs
+++ b/cli/lsp/config.rs
@@ -1697,9 +1697,14 @@ impl ConfigTree {
   }
 
   pub fn is_watched_file(&self, specifier: &ModuleSpecifier) -> bool {
-    if specifier.path().ends_with("/deno.json")
-      || specifier.path().ends_with("/deno.jsonc")
-      || specifier.path().ends_with("/package.json")
+    let path = specifier.path();
+    if path.ends_with("/deno.json")
+      || path.ends_with("/deno.jsonc")
+      || path.ends_with("/package.json")
+      || path.ends_with("/node_modules/.package-lock.json")
+      || path.ends_with("/node_modules/.yarn-integrity.json")
+      || path.ends_with("/node_modules/.modules.yaml")
+      || path.ends_with("/node_modules/.deno/.setup-cache.bin")
     {
       return true;
     }
diff --git a/tests/integration/lsp_tests.rs b/tests/integration/lsp_tests.rs
index 7c7e9315ce..4693b72223 100644
--- a/tests/integration/lsp_tests.rs
+++ b/tests/integration/lsp_tests.rs
@@ -14767,7 +14767,6 @@ fn lsp_byonm() {
       "@denotest/esm-basic": "*",
     },
   }));
-  context.run_npm("install");
   let mut client = context.new_lsp_command().build();
   client.initialize_default();
   let diagnostics = client.did_open(json!({
@@ -14781,6 +14780,51 @@ fn lsp_byonm() {
       "#,
     },
   }));
+  assert_eq!(
+    json!(diagnostics.all()),
+    json!([
+      {
+        "range": {
+          "start": {
+            "line": 1,
+            "character": 15,
+          },
+          "end": {
+            "line": 1,
+            "character": 26,
+          },
+        },
+        "severity": 1,
+        "code": "resolver-error",
+        "source": "deno",
+        "message": "Could not find a matching package for 'npm:chalk' in a package.json file. You must specify this as a package.json dependency when the node_modules folder is not managed by Deno.",
+      },
+      {
+        "range": {
+          "start": {
+            "line": 2,
+            "character": 15,
+          },
+          "end": {
+            "line": 2,
+            "character": 36,
+          },
+        },
+        "severity": 1,
+        "code": "resolver-error",
+        "source": "deno",
+        "message": "Could not resolve \"@denotest/esm-basic\", but found it in a package.json. Deno expects the node_modules/ directory to be up to date. Did you forget to run `deno install`?",
+      },
+    ])
+  );
+  context.run_npm("install");
+  client.did_change_watched_files(json!({
+    "changes": [{
+      "uri": temp_dir.url().join("node_modules/.package-lock.json").unwrap(),
+      "type": 1,
+    }],
+  }));
+  let diagnostics = client.read_diagnostics();
   assert_eq!(
     json!(diagnostics.all()),
     json!([