diff --git a/cli/args/flags.rs b/cli/args/flags.rs
index ee8ec2563a..21a940dc51 100644
--- a/cli/args/flags.rs
+++ b/cli/args/flags.rs
@@ -767,6 +767,7 @@ glob {*_,*.,}bench.{js,mjs,ts,mts,jsx,tsx}:
 
 fn bundle_subcommand<'a>() -> Command<'a> {
   compile_args(Command::new("bundle"))
+    .hide(true)
     .arg(
       Arg::new("source_file")
         .takes_value(true)
diff --git a/cli/tests/integration/watcher_tests.rs b/cli/tests/integration/watcher_tests.rs
index 5ba16cd5e4..99d5a57279 100644
--- a/cli/tests/integration/watcher_tests.rs
+++ b/cli/tests/integration/watcher_tests.rs
@@ -402,6 +402,8 @@ fn bundle_js_watch() {
 
   let (_stdout_lines, mut stderr_lines) = child_lines(&mut deno);
 
+  assert_contains!(stderr_lines.next().unwrap(), "Warning");
+  assert_contains!(stderr_lines.next().unwrap(), "deno_emit");
   assert_contains!(stderr_lines.next().unwrap(), "Check");
   let next_line = stderr_lines.next().unwrap();
   assert_contains!(&next_line, "Bundle started");
@@ -455,8 +457,9 @@ fn bundle_watch_not_exit() {
     .unwrap();
   let (_stdout_lines, mut stderr_lines) = child_lines(&mut deno);
 
-  let next_line = stderr_lines.next().unwrap();
-  assert_contains!(&next_line, "Bundle started");
+  assert_contains!(stderr_lines.next().unwrap(), "Warning");
+  assert_contains!(stderr_lines.next().unwrap(), "deno_emit");
+  assert_contains!(stderr_lines.next().unwrap(), "Bundle started");
   assert_contains!(stderr_lines.next().unwrap(), "error:");
   assert_eq!(stderr_lines.next().unwrap(), "");
   assert_eq!(stderr_lines.next().unwrap(), "  syntax error ^^");
diff --git a/cli/tests/testdata/bundle/shebang_file.bundle.out b/cli/tests/testdata/bundle/shebang_file.bundle.out
index df425f6566..978fe6d97d 100644
--- a/cli/tests/testdata/bundle/shebang_file.bundle.out
+++ b/cli/tests/testdata/bundle/shebang_file.bundle.out
@@ -1,3 +1,5 @@
+Warning "deno bundle" is deprecated and will be removed in the future.
+Use alternative bundlers like "deno_emit", "esbuild" or "rollup" instead.
 Bundle file:///[WILDCARD]/subdir/shebang_file.js
 #!/usr/bin/env -S deno run --allow-read
 // deno-fmt-ignore-file
diff --git a/cli/tools/bundle.rs b/cli/tools/bundle.rs
index 86b28828b8..6a9019cd86 100644
--- a/cli/tools/bundle.rs
+++ b/cli/tools/bundle.rs
@@ -25,6 +25,15 @@ pub async fn bundle(
   bundle_flags: BundleFlags,
 ) -> Result<(), AnyError> {
   let cli_options = Arc::new(CliOptions::from_flags(flags)?);
+
+  log::info!(
+    "{} \"deno bundle\" is deprecated and will be removed in the future.",
+    colors::yellow("Warning"),
+  );
+  log::info!(
+    "Use alternative bundlers like \"deno_emit\", \"esbuild\" or \"rollup\" instead."
+  );
+
   let resolver = |_| {
     let cli_options = cli_options.clone();
     let source_file1 = &bundle_flags.source_file;