diff --git a/cli/main.rs b/cli/main.rs
index 672668c2a84da8..8c27e34b7d40ba 100644
--- a/cli/main.rs
+++ b/cli/main.rs
@@ -492,7 +492,7 @@ async fn install_command(
   let mut worker =
     create_main_worker(&program_state, main_module.clone(), permissions, None);
   // First, fetch and compile the module; this step ensures that the module exists.
-  worker.preload_module(&main_module).await?;
+  worker.preload_module(&main_module, true).await?;
   tools::installer::install(
     flags,
     &install_flags.module_url,
@@ -604,7 +604,7 @@ async fn eval_command(
   // to allow module access by TS compiler.
   program_state.file_fetcher.insert_cached(file);
   debug!("main_module {}", &main_module);
-  worker.execute_module(&main_module).await?;
+  worker.execute_main_module(&main_module).await?;
   worker.execute_script(
     &located_script_name!(),
     "window.dispatchEvent(new Event('load'))",
@@ -862,7 +862,7 @@ async fn run_from_stdin(flags: Flags) -> Result<(), AnyError> {
   program_state.file_fetcher.insert_cached(source_file);
 
   debug!("main_module {}", main_module);
-  worker.execute_module(&main_module).await?;
+  worker.execute_main_module(&main_module).await?;
   worker.execute_script(
     &located_script_name!(),
     "window.dispatchEvent(new Event('load'))",
@@ -949,7 +949,7 @@ async fn run_with_watch(flags: Flags, script: String) -> Result<(), AnyError> {
       &mut self,
       main_module: &ModuleSpecifier,
     ) -> Result<(), AnyError> {
-      self.worker.execute_module(main_module).await?;
+      self.worker.execute_main_module(main_module).await?;
       self.worker.execute_script(
         &located_script_name!(),
         "window.dispatchEvent(new Event('load'))",
@@ -1044,7 +1044,7 @@ async fn run_command(
     };
 
   debug!("main_module {}", main_module);
-  worker.execute_module(&main_module).await?;
+  worker.execute_main_module(&main_module).await?;
   worker.execute_script(
     &located_script_name!(),
     "window.dispatchEvent(new Event('load'))",
diff --git a/cli/standalone.rs b/cli/standalone.rs
index a3ace49f7ad916..19132723ce158c 100644
--- a/cli/standalone.rs
+++ b/cli/standalone.rs
@@ -271,7 +271,7 @@ pub async fn run(
     js_runtime.sync_ops_cache();
   }
   worker.bootstrap(&options);
-  worker.execute_module(&main_module).await?;
+  worker.execute_main_module(&main_module).await?;
   worker.execute_script(
     &located_script_name!(),
     "window.dispatchEvent(new Event('load'))",
diff --git a/cli/tools/test.rs b/cli/tools/test.rs
index a807bde0552aa6..0113f1e387bf9f 100644
--- a/cli/tools/test.rs
+++ b/cli/tools/test.rs
@@ -306,7 +306,7 @@ async fn test_specifier(
     None
   };
 
-  worker.execute_module(&test_specifier).await?;
+  worker.execute_main_module(&test_specifier).await?;
 
   worker.js_runtime.execute_script(
     &located_script_name!(),
diff --git a/core/modules.rs b/core/modules.rs
index f1f083fe9f7d14..a21e974647b0db 100644
--- a/core/modules.rs
+++ b/core/modules.rs
@@ -186,6 +186,8 @@ impl ModuleLoader for FsModuleLoader {
 enum LoadInit {
   /// Main module specifier.
   Main(String),
+  /// Module specifier for side module.
+  Side(String),
   /// Dynamic import specifier with referrer.
   DynamicImport(String, String),
 }
@@ -221,6 +223,10 @@ impl RecursiveModuleLoad {
     Self::new(LoadInit::Main(specifier.to_string()), module_map_rc)
   }
 
+  pub fn side(specifier: &str, module_map_rc: Rc<RefCell<ModuleMap>>) -> Self {
+    Self::new(LoadInit::Side(specifier.to_string()), module_map_rc)
+  }
+
   pub fn dynamic_import(
     specifier: &str,
     referrer: &str,
@@ -267,6 +273,11 @@ impl RecursiveModuleLoad {
           .loader
           .resolve(self.op_state.clone(), specifier, ".", true)
       }
+      LoadInit::Side(ref specifier) => {
+        self
+          .loader
+          .resolve(self.op_state.clone(), specifier, ".", false)
+      }
       LoadInit::DynamicImport(ref specifier, ref referrer) => self
         .loader
         .resolve(self.op_state.clone(), specifier, referrer, false),
@@ -283,6 +294,13 @@ impl RecursiveModuleLoad {
             .resolve(op_state.clone(), specifier, ".", true)?;
         (spec, None)
       }
+      LoadInit::Side(ref specifier) => {
+        let spec =
+          self
+            .loader
+            .resolve(op_state.clone(), specifier, ".", false)?;
+        (spec, None)
+      }
       LoadInit::DynamicImport(ref specifier, ref referrer) => {
         let spec =
           self
@@ -305,7 +323,9 @@ impl RecursiveModuleLoad {
   }
 
   pub fn is_currently_loading_main_module(&self) -> bool {
-    !self.is_dynamic_import() && self.state == LoadState::LoadingRoot
+    !self.is_dynamic_import()
+      && matches!(self.init, LoadInit::Main(..))
+      && self.state == LoadState::LoadingRoot
   }
 
   pub fn register_and_recurse(
@@ -575,6 +595,17 @@ impl ModuleMap {
       import_specifiers.push(module_specifier);
     }
 
+    if main {
+      let maybe_main_module = self.info.values().find(|module| module.main);
+      if let Some(main_module) = maybe_main_module {
+        return Err(generic_error(
+          format!("Trying to create \"main\" module ({:?}), when one already exists ({:?})",
+          name,
+          main_module.name,
+        )));
+      }
+    }
+
     let handle = v8::Global::<v8::Module>::new(tc_scope, module);
     let id = self.next_module_id;
     self.next_module_id += 1;
@@ -644,6 +675,15 @@ impl ModuleMap {
     Ok(load)
   }
 
+  pub async fn load_side(
+    module_map_rc: Rc<RefCell<ModuleMap>>,
+    specifier: &str,
+  ) -> Result<RecursiveModuleLoad, AnyError> {
+    let load = RecursiveModuleLoad::side(specifier, module_map_rc.clone());
+    load.prepare().await?;
+    Ok(load)
+  }
+
   // Initiate loading of a module graph imported using `import()`.
   pub fn load_dynamic_import(
     module_map_rc: Rc<RefCell<ModuleMap>>,
@@ -903,7 +943,7 @@ mod tests {
       ..Default::default()
     });
     let spec = crate::resolve_url("file:///a.js").unwrap();
-    let a_id_fut = runtime.load_module(&spec, None);
+    let a_id_fut = runtime.load_main_module(&spec, None);
     let a_id = futures::executor::block_on(a_id_fut).expect("Failed to load");
 
     let _ = runtime.mod_evaluate(a_id);
@@ -1363,7 +1403,7 @@ mod tests {
 
     let fut = async move {
       let spec = crate::resolve_url("file:///circular1.js").unwrap();
-      let result = runtime.load_module(&spec, None).await;
+      let result = runtime.load_main_module(&spec, None).await;
       assert!(result.is_ok());
       let circular1_id = result.unwrap();
       let _ = runtime.mod_evaluate(circular1_id);
@@ -1435,7 +1475,7 @@ mod tests {
 
     let fut = async move {
       let spec = crate::resolve_url("file:///redirect1.js").unwrap();
-      let result = runtime.load_module(&spec, None).await;
+      let result = runtime.load_main_module(&spec, None).await;
       println!(">> result {:?}", result);
       assert!(result.is_ok());
       let redirect1_id = result.unwrap();
@@ -1500,7 +1540,8 @@ mod tests {
         ..Default::default()
       });
       let spec = crate::resolve_url("file:///main.js").unwrap();
-      let mut recursive_load = runtime.load_module(&spec, None).boxed_local();
+      let mut recursive_load =
+        runtime.load_main_module(&spec, None).boxed_local();
 
       let result = recursive_load.poll_unpin(&mut cx);
       assert!(result.is_pending());
@@ -1548,7 +1589,7 @@ mod tests {
         ..Default::default()
       });
       let spec = crate::resolve_url("file:///bad_import.js").unwrap();
-      let mut load_fut = runtime.load_module(&spec, None).boxed_local();
+      let mut load_fut = runtime.load_main_module(&spec, None).boxed_local();
       let result = load_fut.poll_unpin(&mut cx);
       if let Poll::Ready(Err(err)) = result {
         assert_eq!(
@@ -1583,7 +1624,7 @@ mod tests {
     // The behavior should be very similar to /a.js.
     let spec = crate::resolve_url("file:///main_with_code.js").unwrap();
     let main_id_fut = runtime
-      .load_module(&spec, Some(MAIN_WITH_CODE_SRC.to_owned()))
+      .load_main_module(&spec, Some(MAIN_WITH_CODE_SRC.to_owned()))
       .boxed_local();
     let main_id =
       futures::executor::block_on(main_id_fut).expect("Failed to load");
@@ -1622,4 +1663,80 @@ mod tests {
     );
     assert_eq!(modules.get_children(d_id), Some(&vec![]));
   }
+
+  #[test]
+  fn main_and_side_module() {
+    struct ModsLoader {}
+
+    let main_specifier = crate::resolve_url("file:///main_module.js").unwrap();
+    let side_specifier = crate::resolve_url("file:///side_module.js").unwrap();
+
+    impl ModuleLoader for ModsLoader {
+      fn resolve(
+        &self,
+        _op_state: Rc<RefCell<OpState>>,
+        specifier: &str,
+        referrer: &str,
+        _is_main: bool,
+      ) -> Result<ModuleSpecifier, AnyError> {
+        let s = crate::resolve_import(specifier, referrer).unwrap();
+        Ok(s)
+      }
+
+      fn load(
+        &self,
+        _op_state: Rc<RefCell<OpState>>,
+        module_specifier: &ModuleSpecifier,
+        _maybe_referrer: Option<ModuleSpecifier>,
+        _is_dyn_import: bool,
+      ) -> Pin<Box<ModuleSourceFuture>> {
+        let module_source = match module_specifier.as_str() {
+          "file:///main_module.js" => Ok(ModuleSource {
+            module_url_specified: "file:///main_module.js".to_string(),
+            module_url_found: "file:///main_module.js".to_string(),
+            code: "if (!import.meta.main) throw Error();".to_owned(),
+          }),
+          "file:///side_module.js" => Ok(ModuleSource {
+            module_url_specified: "file:///side_module.js".to_string(),
+            module_url_found: "file:///side_module.js".to_string(),
+            code: "if (import.meta.main) throw Error();".to_owned(),
+          }),
+          _ => unreachable!(),
+        };
+        async move { module_source }.boxed()
+      }
+    }
+
+    let loader = Rc::new(ModsLoader {});
+    let mut runtime = JsRuntime::new(RuntimeOptions {
+      module_loader: Some(loader),
+      ..Default::default()
+    });
+
+    let main_id_fut = runtime
+      .load_main_module(&main_specifier, None)
+      .boxed_local();
+    let main_id =
+      futures::executor::block_on(main_id_fut).expect("Failed to load");
+
+    let _ = runtime.mod_evaluate(main_id);
+    futures::executor::block_on(runtime.run_event_loop(false)).unwrap();
+
+    // Try to add another main module - it should error.
+    let side_id_fut = runtime
+      .load_main_module(&side_specifier, None)
+      .boxed_local();
+    futures::executor::block_on(side_id_fut)
+      .expect_err("Should have failed to load second main module");
+
+    // And now try to load it as a side module
+    let side_id_fut = runtime
+      .load_side_module(&side_specifier, None)
+      .boxed_local();
+    let side_id =
+      futures::executor::block_on(side_id_fut).expect("Failed to load");
+
+    let _ = runtime.mod_evaluate(side_id);
+    futures::executor::block_on(runtime.run_event_loop(false)).unwrap();
+  }
 }
diff --git a/core/runtime.rs b/core/runtime.rs
index d5089569d2f3ae..f2e804abb13e23 100644
--- a/core/runtime.rs
+++ b/core/runtime.rs
@@ -1350,11 +1350,14 @@ impl JsRuntime {
     state_rc.borrow_mut().pending_dyn_mod_evaluate = still_pending;
   }
 
-  /// Asynchronously load specified module and all of its dependencies
+  /// Asynchronously load specified module and all of its dependencies.
+  ///
+  /// The module will be marked as "main", and because of that
+  /// "import.meta.main" will return true when checked inside that module.
   ///
   /// User must call `JsRuntime::mod_evaluate` with returned `ModuleId`
   /// manually after load is finished.
-  pub async fn load_module(
+  pub async fn load_main_module(
     &mut self,
     specifier: &ModuleSpecifier,
     code: Option<String>,
@@ -1363,6 +1366,7 @@ impl JsRuntime {
     if let Some(code) = code {
       module_map_rc.borrow_mut().new_module(
         &mut self.handle_scope(),
+        // main module
         true,
         specifier.as_str(),
         &code,
@@ -1383,6 +1387,59 @@ impl JsRuntime {
     Ok(root_id)
   }
 
+  /// Asynchronously load specified ES module and all of its dependencies.
+  ///
+  /// This method is meant to be used when loading some utility code that
+  /// might be later imported by the main module (ie. an entry point module).
+  ///
+  /// User must call `JsRuntime::mod_evaluate` with returned `ModuleId`
+  /// manually after load is finished.
+  pub async fn load_side_module(
+    &mut self,
+    specifier: &ModuleSpecifier,
+    code: Option<String>,
+  ) -> Result<ModuleId, AnyError> {
+    let module_map_rc = Self::module_map(self.v8_isolate());
+    if let Some(code) = code {
+      module_map_rc.borrow_mut().new_module(
+        &mut self.handle_scope(),
+        // not main module
+        false,
+        specifier.as_str(),
+        &code,
+      )?;
+    }
+
+    let mut load =
+      ModuleMap::load_side(module_map_rc.clone(), specifier.as_str()).await?;
+
+    while let Some(info_result) = load.next().await {
+      let info = info_result?;
+      let scope = &mut self.handle_scope();
+      load.register_and_recurse(scope, &info)?;
+    }
+
+    let root_id = load.root_module_id.expect("Root module should be loaded");
+    self.instantiate_module(root_id)?;
+    Ok(root_id)
+  }
+
+  /// Asynchronously load specified module and all of its dependencies
+  ///
+  /// User must call `JsRuntime::mod_evaluate` with returned `ModuleId`
+  /// manually after load is finished.
+  #[deprecated(
+    since = "0.100.0",
+    note = "This method had a bug, marking multiple modules loaded as \"main\". Use `load_main_module` or `load_side_module` instead."
+  )]
+  pub async fn load_module(
+    &mut self,
+    specifier: &ModuleSpecifier,
+    code: Option<String>,
+  ) -> Result<ModuleId, AnyError> {
+    self.load_main_module(specifier, code).await
+  }
+
   fn poll_pending_ops(
     &mut self,
     cx: &mut Context,
@@ -2040,7 +2097,7 @@ pub mod tests {
     let source_code = "Deno.core.print('hello\\n')".to_string();
 
     let module_id = futures::executor::block_on(
-      runtime.load_module(&specifier, Some(source_code)),
+      runtime.load_main_module(&specifier, Some(source_code)),
     )
     .unwrap();
 
diff --git a/runtime/examples/hello_runtime.rs b/runtime/examples/hello_runtime.rs
index 9ac1d0a273c906..db63946941f985 100644
--- a/runtime/examples/hello_runtime.rs
+++ b/runtime/examples/hello_runtime.rs
@@ -57,7 +57,7 @@ async fn main() -> Result<(), AnyError> {
   let mut worker =
     MainWorker::from_options(main_module.clone(), permissions, &options);
   worker.bootstrap(&options);
-  worker.execute_module(&main_module).await?;
+  worker.execute_main_module(&main_module).await?;
   worker.run_event_loop(false).await?;
   Ok(())
 }
diff --git a/runtime/web_worker.rs b/runtime/web_worker.rs
index ed7b95f5bab735..975028b16921f9 100644
--- a/runtime/web_worker.rs
+++ b/runtime/web_worker.rs
@@ -458,21 +458,32 @@ impl WebWorker {
     Ok(())
   }
 
-  /// Loads and instantiates specified JavaScript module.
+  /// Loads and instantiates specified JavaScript module
+  /// as "main" or "side" module.
   pub async fn preload_module(
     &mut self,
     module_specifier: &ModuleSpecifier,
+    main: bool,
   ) -> Result<ModuleId, AnyError> {
-    self.js_runtime.load_module(module_specifier, None).await
+    if main {
+      self
+        .js_runtime
+        .load_main_module(module_specifier, None)
+        .await
+    } else {
+      self
+        .js_runtime
+        .load_side_module(module_specifier, None)
+        .await
+    }
   }
 
   /// Loads, instantiates and executes specified JavaScript module.
-  pub async fn execute_module(
+  pub async fn execute_main_module(
     &mut self,
     module_specifier: &ModuleSpecifier,
   ) -> Result<(), AnyError> {
-    let id = self.preload_module(module_specifier).await?;
-
+    let id = self.preload_module(module_specifier, true).await?;
     let mut receiver = self.js_runtime.mod_evaluate(id);
     tokio::select! {
       maybe_result = &mut receiver => {
@@ -494,6 +505,17 @@ impl WebWorker {
     }
   }
 
+  #[deprecated(
+    since = "0.26.0",
+    note = "This method had a bug, marking multiple modules loaded as \"main\". Use `execute_main_module`."
+  )]
+  pub async fn execute_module(
+    &mut self,
+    module_specifier: &ModuleSpecifier,
+  ) -> Result<(), AnyError> {
+    self.execute_main_module(module_specifier).await
+  }
+
   pub fn poll_event_loop(
     &mut self,
     cx: &mut Context,
@@ -568,7 +590,7 @@ pub fn run_web_worker(
     } else {
       // TODO(bartlomieju): add "type": "classic", ie. ability to load
       // script instead of module
-      worker.execute_module(&specifier).await
+      worker.execute_main_module(&specifier).await
     };
 
     let internal_handle = worker.internal_handle.clone();
diff --git a/runtime/worker.rs b/runtime/worker.rs
index 92bebe92a9e2e4..54b8a8d6845776 100644
--- a/runtime/worker.rs
+++ b/runtime/worker.rs
@@ -207,21 +207,27 @@ impl MainWorker {
     Ok(())
   }
 
-  /// Loads and instantiates specified JavaScript module.
+  /// Loads and instantiates specified JavaScript module
+  /// as "main" or "side" module.
   pub async fn preload_module(
     &mut self,
     module_specifier: &ModuleSpecifier,
+    main: bool,
   ) -> Result<ModuleId, AnyError> {
-    self.js_runtime.load_module(module_specifier, None).await
+    if main {
+      self
+        .js_runtime
+        .load_main_module(module_specifier, None)
+        .await
+    } else {
+      self
+        .js_runtime
+        .load_side_module(module_specifier, None)
+        .await
+    }
   }
 
-  /// Loads, instantiates and executes specified JavaScript module.
-  pub async fn execute_module(
-    &mut self,
-    module_specifier: &ModuleSpecifier,
-  ) -> Result<(), AnyError> {
-    let id = self.preload_module(module_specifier).await?;
-    self.wait_for_inspector_session();
+  async fn evaluate_module(&mut self, id: ModuleId) -> Result<(), AnyError> {
     let mut receiver = self.js_runtime.mod_evaluate(id);
     tokio::select! {
       maybe_result = &mut receiver => {
@@ -237,6 +243,38 @@ impl MainWorker {
     }
   }
 
+  /// Loads, instantiates and executes specified JavaScript module.
+  pub async fn execute_side_module(
+    &mut self,
+    module_specifier: &ModuleSpecifier,
+  ) -> Result<(), AnyError> {
+    let id = self.preload_module(module_specifier, false).await?;
+    self.evaluate_module(id).await
+  }
+
+  /// Loads, instantiates and executes specified JavaScript module.
+  ///
+  /// This module will have "import.meta.main" equal to true.
+  pub async fn execute_main_module(
+    &mut self,
+    module_specifier: &ModuleSpecifier,
+  ) -> Result<(), AnyError> {
+    let id = self.preload_module(module_specifier, true).await?;
+    self.wait_for_inspector_session();
+    self.evaluate_module(id).await
+  }
+
+  #[deprecated(
+    since = "0.26.0",
+    note = "This method had a bug, marking multiple modules loaded as \"main\". Use `execute_main_module` or `execute_side_module` instead."
+  )]
+  pub async fn execute_module(
+    &mut self,
+    module_specifier: &ModuleSpecifier,
+  ) -> Result<(), AnyError> {
+    self.execute_main_module(module_specifier).await
+  }
+
   fn wait_for_inspector_session(&mut self) {
     if self.should_break_on_first_statement {
       self
@@ -330,7 +368,7 @@ mod tests {
     let p = test_util::testdata_path().join("esm_imports_a.js");
     let module_specifier = resolve_url_or_path(&p.to_string_lossy()).unwrap();
     let mut worker = create_test_worker();
-    let result = worker.execute_module(&module_specifier).await;
+    let result = worker.execute_main_module(&module_specifier).await;
     if let Err(err) = result {
       eprintln!("execute_mod err {:?}", err);
     }
@@ -347,7 +385,7 @@ mod tests {
       .join("tests/circular1.js");
     let module_specifier = resolve_url_or_path(&p.to_string_lossy()).unwrap();
     let mut worker = create_test_worker();
-    let result = worker.execute_module(&module_specifier).await;
+    let result = worker.execute_main_module(&module_specifier).await;
     if let Err(err) = result {
       eprintln!("execute_mod err {:?}", err);
     }
@@ -361,7 +399,7 @@ mod tests {
     // "foo" is not a valid module specifier so this should return an error.
     let mut worker = create_test_worker();
     let module_specifier = resolve_url_or_path("does-not-exist").unwrap();
-    let result = worker.execute_module(&module_specifier).await;
+    let result = worker.execute_main_module(&module_specifier).await;
     assert!(result.is_err());
   }
 
@@ -372,7 +410,7 @@ mod tests {
     let mut worker = create_test_worker();
     let p = test_util::testdata_path().join("001_hello.js");
     let module_specifier = resolve_url_or_path(&p.to_string_lossy()).unwrap();
-    let result = worker.execute_module(&module_specifier).await;
+    let result = worker.execute_main_module(&module_specifier).await;
     assert!(result.is_ok());
   }
 }