diff --git a/bench_util/js_runtime.rs b/bench_util/js_runtime.rs
index f87fa3b03a..0495d6d8dc 100644
--- a/bench_util/js_runtime.rs
+++ b/bench_util/js_runtime.rs
@@ -9,7 +9,7 @@ use crate::profiling::is_profiling;
 
 pub fn create_js_runtime(setup: impl FnOnce() -> Vec<Extension>) -> JsRuntime {
   JsRuntime::new(RuntimeOptions {
-    extensions: setup(),
+    extensions_with_js: setup(),
     ..Default::default()
   })
 }
diff --git a/cli/build.rs b/cli/build.rs
index 15be033fd8..4865cadb56 100644
--- a/cli/build.rs
+++ b/cli/build.rs
@@ -243,6 +243,7 @@ mod ts {
           Ok(())
         })
         .build()],
+      extensions_with_js: vec![],
       additional_files: files,
       compression_cb: Some(Box::new(|vec, snapshot_slice| {
         vec.extend_from_slice(
@@ -304,6 +305,7 @@ fn create_cli_snapshot(snapshot_path: PathBuf, files: Vec<PathBuf>) {
     snapshot_path,
     startup_snapshot: Some(deno_runtime::js::deno_isolate_init()),
     extensions,
+    extensions_with_js: vec![],
     additional_files: files,
     compression_cb: Some(Box::new(|vec, snapshot_slice| {
       lzzzz::lz4_hc::compress_to_vec(
diff --git a/core/runtime.rs b/core/runtime.rs
index 9ee3aad70c..5272266260 100644
--- a/core/runtime.rs
+++ b/core/runtime.rs
@@ -87,6 +87,7 @@ pub struct JsRuntime {
   built_from_snapshot: bool,
   allocations: IsolateAllocations,
   extensions: Vec<Extension>,
+  extensions_with_js: Vec<Extension>,
   event_loop_middlewares: Vec<Box<OpEventLoopFn>>,
   // Marks if this is considered the top-level runtime. Used only be inspector.
   is_main: bool,
@@ -240,10 +241,23 @@ pub struct RuntimeOptions {
   /// executed tries to load modules.
   pub module_loader: Option<Rc<dyn ModuleLoader>>,
 
-  /// JsRuntime extensions, not to be confused with ES modules
-  /// these are sets of ops and other JS code to be initialized.
+  /// JsRuntime extensions, not to be confused with ES modules.
+  /// Only ops registered by extensions will be initialized. If you need
+  /// to execute JS code from extensions, use `extensions_with_js` options
+  /// instead.
   pub extensions: Vec<Extension>,
 
+  /// JsRuntime extensions, not to be confused with ES modules.
+  /// Ops registered by extensions will be initialized and JS code will be
+  /// executed. If you don't need to execute JS code from extensions, use
+  /// `extensions` option instead.
+  ///
+  /// This is useful when creating snapshots, in such case you would pass
+  /// extensions using `extensions_with_js`, later when creating a runtime
+  /// from the snapshot, you would pass these extensions using `extensions`
+  /// option.
+  pub extensions_with_js: Vec<Extension>,
+
   /// V8 snapshot that should be loaded on startup.
   ///
   /// Currently can't be used with `will_snapshot`.
@@ -339,11 +353,20 @@ impl JsRuntime {
     let has_startup_snapshot = options.startup_snapshot.is_some();
 
     // Add builtins extension
-    options
-      .extensions
-      .insert(0, crate::ops_builtin::init_builtins());
+    if !has_startup_snapshot {
+      options
+        .extensions_with_js
+        .insert(0, crate::ops_builtin::init_builtins());
+    } else {
+      options
+        .extensions
+        .insert(0, crate::ops_builtin::init_builtins());
+    }
 
-    let ops = Self::collect_ops(&mut options.extensions);
+    let ops = Self::collect_ops(
+      &mut options.extensions,
+      &mut options.extensions_with_js,
+    );
     let mut op_state = OpState::new(ops.len());
 
     if let Some(get_error_class_fn) = options.get_error_class_fn {
@@ -539,6 +562,7 @@ impl JsRuntime {
       allocations: IsolateAllocations::default(),
       event_loop_middlewares: Vec::with_capacity(options.extensions.len()),
       extensions: options.extensions,
+      extensions_with_js: options.extensions_with_js,
       state: state_rc,
       module_map: Some(module_map_rc),
       is_main: options.is_main,
@@ -547,12 +571,8 @@ impl JsRuntime {
     // Init resources and ops before extensions to make sure they are
     // available during the initialization process.
     js_runtime.init_extension_ops().unwrap();
-    // TODO(@AaronO): diff extensions inited in snapshot and those provided
-    // for now we assume that snapshot and extensions always match
-    if !has_startup_snapshot {
-      let realm = js_runtime.global_realm();
-      js_runtime.init_extension_js(&realm).unwrap();
-    }
+    let realm = js_runtime.global_realm();
+    js_runtime.init_extension_js(&realm).unwrap();
     // Init callbacks (opresolve)
     js_runtime.init_cbs();
 
@@ -682,7 +702,8 @@ impl JsRuntime {
   /// Initializes JS of provided Extensions in the given realm
   fn init_extension_js(&mut self, realm: &JsRealm) -> Result<(), Error> {
     // Take extensions to avoid double-borrow
-    let mut extensions: Vec<Extension> = std::mem::take(&mut self.extensions);
+    let mut extensions: Vec<Extension> =
+      std::mem::take(&mut self.extensions_with_js);
     for m in extensions.iter_mut() {
       let js_files = m.init_js();
       for (filename, source) in js_files {
@@ -691,15 +712,22 @@ impl JsRuntime {
       }
     }
     // Restore extensions
-    self.extensions = extensions;
+    self.extensions_with_js = extensions;
 
     Ok(())
   }
 
   /// Collects ops from extensions & applies middleware
-  fn collect_ops(extensions: &mut [Extension]) -> Vec<OpDecl> {
+  fn collect_ops(
+    extensions: &mut [Extension],
+    extensions_with_js: &mut [Extension],
+  ) -> Vec<OpDecl> {
+    let mut exts = vec![];
+    exts.extend(extensions);
+    exts.extend(extensions_with_js);
+
     // Middleware
-    let middleware: Vec<Box<OpMiddlewareFn>> = extensions
+    let middleware: Vec<Box<OpMiddlewareFn>> = exts
       .iter_mut()
       .filter_map(|e| e.init_middleware())
       .collect();
@@ -708,7 +736,7 @@ impl JsRuntime {
     let macroware = move |d| middleware.iter().fold(d, |d, m| m(d));
 
     // Flatten ops, apply middlware & override disabled ops
-    extensions
+    exts
       .iter_mut()
       .filter_map(|e| e.init_ops())
       .flatten()
@@ -733,22 +761,41 @@ impl JsRuntime {
   fn init_extension_ops(&mut self) -> Result<(), Error> {
     let op_state = self.op_state();
     // Take extensions to avoid double-borrow
-    let mut extensions: Vec<Extension> = std::mem::take(&mut self.extensions);
+    {
+      let mut extensions: Vec<Extension> = std::mem::take(&mut self.extensions);
 
-    // Setup state
-    for e in extensions.iter_mut() {
-      // ops are already registered during in bindings::initialize_context();
-      e.init_state(&mut op_state.borrow_mut())?;
+      // Setup state
+      for e in extensions.iter_mut() {
+        // ops are already registered during in bindings::initialize_context();
+        e.init_state(&mut op_state.borrow_mut())?;
 
-      // Setup event-loop middleware
-      if let Some(middleware) = e.init_event_loop_middleware() {
-        self.event_loop_middlewares.push(middleware);
+        // Setup event-loop middleware
+        if let Some(middleware) = e.init_event_loop_middleware() {
+          self.event_loop_middlewares.push(middleware);
+        }
       }
+
+      // Restore extensions
+      self.extensions = extensions;
     }
+    {
+      let mut extensions: Vec<Extension> =
+        std::mem::take(&mut self.extensions_with_js);
 
-    // Restore extensions
-    self.extensions = extensions;
+      // Setup state
+      for e in extensions.iter_mut() {
+        // ops are already registered during in bindings::initialize_context();
+        e.init_state(&mut op_state.borrow_mut())?;
 
+        // Setup event-loop middleware
+        if let Some(middleware) = e.init_event_loop_middleware() {
+          self.event_loop_middlewares.push(middleware);
+        }
+      }
+
+      // Restore extensions
+      self.extensions_with_js = extensions;
+    }
     Ok(())
   }
 
diff --git a/core/snapshot_util.rs b/core/snapshot_util.rs
index b408bad564..bacc0c6aeb 100644
--- a/core/snapshot_util.rs
+++ b/core/snapshot_util.rs
@@ -12,6 +12,7 @@ pub struct CreateSnapshotOptions {
   pub snapshot_path: PathBuf,
   pub startup_snapshot: Option<Snapshot>,
   pub extensions: Vec<Extension>,
+  pub extensions_with_js: Vec<Extension>,
   pub additional_files: Vec<PathBuf>,
   pub compression_cb: Option<Box<CompressionCb>>,
 }
@@ -21,6 +22,7 @@ pub fn create_snapshot(create_snapshot_options: CreateSnapshotOptions) {
     will_snapshot: true,
     startup_snapshot: create_snapshot_options.startup_snapshot,
     extensions: create_snapshot_options.extensions,
+    extensions_with_js: create_snapshot_options.extensions_with_js,
     ..Default::default()
   });
 
diff --git a/runtime/build.rs b/runtime/build.rs
index bab7745cc3..62a3da03b8 100644
--- a/runtime/build.rs
+++ b/runtime/build.rs
@@ -120,7 +120,7 @@ mod not_docs {
   }
 
   fn create_runtime_snapshot(snapshot_path: PathBuf, files: Vec<PathBuf>) {
-    let extensions: Vec<Extension> = vec![
+    let extensions_with_js: Vec<Extension> = vec![
       deno_webidl::init(),
       deno_console::init(),
       deno_url::init(),
@@ -154,7 +154,8 @@ mod not_docs {
       cargo_manifest_dir: env!("CARGO_MANIFEST_DIR"),
       snapshot_path,
       startup_snapshot: None,
-      extensions,
+      extensions: vec![],
+      extensions_with_js,
       additional_files: files,
       compression_cb: Some(Box::new(|vec, snapshot_slice| {
         lzzzz::lz4_hc::compress_to_vec(