diff --git a/internal/bundler/bundler.go b/internal/bundler/bundler.go
index 62c34313166..733ac9ad826 100644
--- a/internal/bundler/bundler.go
+++ b/internal/bundler/bundler.go
@@ -703,7 +703,7 @@ func runOnResolvePlugins(
 	result := res.Resolve(absResolveDir, path, kind)
 
 	// Warn when the case used for importing differs from the actual file name
-	if result != nil && result.DifferentCase != nil {
+	if result != nil && result.DifferentCase != nil && !resolver.IsInsideNodeModules(absResolveDir) {
 		diffCase := *result.DifferentCase
 		log.AddRangeWarning(importSource, importPathRange, fmt.Sprintf(
 			"Use %q instead of %q to avoid issues with case-sensitive file systems",
@@ -935,7 +935,7 @@ func (s *scanner) maybeParseFile(
 	}
 
 	// Don't emit warnings for code inside a "node_modules" directory
-	if resolver.IsInsideNodeModules(s.fs, path.Text) {
+	if resolver.IsInsideNodeModules(path.Text) {
 		optionsClone.SuppressWarningsAboutWeirdCode = true
 	}
 
diff --git a/internal/resolver/resolver.go b/internal/resolver/resolver.go
index 2b5ec0b9995..872569080a6 100644
--- a/internal/resolver/resolver.go
+++ b/internal/resolver/resolver.go
@@ -282,7 +282,7 @@ func (r *resolver) ProbeResolvePackageAsRelative(sourceDir string, importPath st
 	return nil
 }
 
-func IsInsideNodeModules(fs fs.FS, path string) bool {
+func IsInsideNodeModules(path string) bool {
 	for {
 		// This is written in a platform-independent manner because it's run on
 		// user-specified paths which can be arbitrary non-file-system things. So
@@ -730,7 +730,7 @@ func (r *resolver) parseTSConfig(file string, visited map[string]bool) (*TSConfi
 		}
 
 		// Suppress warnings about missing base config files inside "node_modules"
-		if !IsInsideNodeModules(r.fs, file) {
+		if !IsInsideNodeModules(file) {
 			r.log.AddRangeWarning(&source, extendsRange,
 				fmt.Sprintf("Cannot find base config file %q", extends))
 		}
diff --git a/scripts/end-to-end-tests.js b/scripts/end-to-end-tests.js
index b77077c5c24..de42f2627b2 100644
--- a/scripts/end-to-end-tests.js
+++ b/scripts/end-to-end-tests.js
@@ -2471,33 +2471,69 @@
     tests.push(
       test(['in.js', '--bundle', '--outfile=node.js'], {
         'in.js': `
-        import x from "./File1.js"
-        import y from "./file2.js"
-        if (x !== 123 || y !== 234) throw 'fail'
-      `,
+          import x from "./File1.js"
+          import y from "./file2.js"
+          if (x !== 123 || y !== 234) throw 'fail'
+        `,
         'file1.js': `export default 123`,
         'File2.js': `export default 234`,
       }, {
         expectedStderr: ` > in.js: warning: Use "file1.js" instead of "File1.js" to avoid issues with case-sensitive file systems
-    2 │         import x from "./File1.js"
-      ╵                       ~~~~~~~~~~~~
+    2 │           import x from "./File1.js"
+      ╵                         ~~~~~~~~~~~~
 
  > in.js: warning: Use "File2.js" instead of "file2.js" to avoid issues with case-sensitive file systems
-    3 │         import y from "./file2.js"
-      ╵                       ~~~~~~~~~~~~
+    3 │           import y from "./file2.js"
+      ╵                         ~~~~~~~~~~~~
 
 2 warnings
 `,
       }),
       test(['in.js', '--bundle', '--outfile=node.js'], {
         'in.js': `
-        import x from "./Dir1/file.js"
-        import y from "./dir2/file.js"
-        if (x !== 123 || y !== 234) throw 'fail'
-      `,
+          import x from "./Dir1/file.js"
+          import y from "./dir2/file.js"
+          if (x !== 123 || y !== 234) throw 'fail'
+        `,
         'dir1/file.js': `export default 123`,
         'Dir2/file.js': `export default 234`,
       }),
+
+      // Warn when importing something inside node_modules
+      test(['in.js', '--bundle', '--outfile=node.js'], {
+        'in.js': `
+          import x from "pkg/File1.js"
+          import y from "pkg/file2.js"
+          if (x !== 123 || y !== 234) throw 'fail'
+        `,
+        'node_modules/pkg/file1.js': `export default 123`,
+        'node_modules/pkg/File2.js': `export default 234`,
+      }, {
+        expectedStderr: ` > in.js: warning: Use "node_modules/pkg/file1.js" instead of "node_modules/pkg/File1.js" to avoid issues with case-sensitive file systems
+    2 │           import x from "pkg/File1.js"
+      ╵                         ~~~~~~~~~~~~~~
+
+ > in.js: warning: Use "node_modules/pkg/File2.js" instead of "node_modules/pkg/file2.js" to avoid issues with case-sensitive file systems
+    3 │           import y from "pkg/file2.js"
+      ╵                         ~~~~~~~~~~~~~~
+
+2 warnings
+`,
+      }),
+
+      // Don't warn when the importer is inside node_modules
+      test(['in.js', '--bundle', '--outfile=node.js'], {
+        'in.js': `
+          import {x, y} from "pkg"
+          if (x !== 123 || y !== 234) throw 'fail'
+        `,
+        'node_modules/pkg/index.js': `
+          export {default as x} from "./File1.js"
+          export {default as y} from "./file2.js"
+        `,
+        'node_modules/pkg/file1.js': `export default 123`,
+        'node_modules/pkg/File2.js': `export default 234`,
+      }),
     )
   }