diff --git a/oak/server/rust/oak_runtime/src/node/logger.rs b/oak/server/rust/oak_runtime/src/node/logger.rs
index 6b360c005af..217ef5f9c8e 100644
--- a/oak/server/rust/oak_runtime/src/node/logger.rs
+++ b/oak/server/rust/oak_runtime/src/node/logger.rs
@@ -87,10 +87,7 @@ fn logger(
         // in case a Wasm node wants to emit remaining messages. We will return once the channel is
         // closed.
 
-        // TODO(#646): Temporarily don't wait for messages when terminating. Renable when channels
-        // track their channels and make sure all channels are closed.
-        // let _ = runtime.wait_on_channels(&[Some(&reader)]);
-        runtime.wait_on_channels(node_id, &[Some(reader)])?;
+        let _ = runtime.wait_on_channels(node_id, &[Some(reader)]);
 
         if let Some(message) = runtime.channel_read(node_id, reader)? {
             match LogMessage::decode(&*message.data) {
diff --git a/oak/server/rust/oak_runtime/src/runtime/channel.rs b/oak/server/rust/oak_runtime/src/runtime/channel.rs
index 04049650873..c407e287986 100644
--- a/oak/server/rust/oak_runtime/src/runtime/channel.rs
+++ b/oak/server/rust/oak_runtime/src/runtime/channel.rs
@@ -20,6 +20,7 @@ use std::sync::atomic::Ordering::SeqCst;
 use std::sync::{Arc, Mutex, RwLock, Weak};
 use std::thread::{Thread, ThreadId};
 
+use log::debug;
 use rand::RngCore;
 
 use oak_abi::OakStatus;
@@ -111,6 +112,12 @@ impl Channel {
         self.readers.load(SeqCst) == 0 || self.writers.load(SeqCst) == 0
     }
 
+    /// Thread safe method that returns true when there is no longer at least one reader or
+    /// writer.
+    pub fn has_no_reference(&self) -> bool {
+        self.readers.load(SeqCst) == 0 && self.writers.load(SeqCst) == 0
+    }
+
     /// Insert the given `thread` reference into `thread_id` slot of the HashMap of waiting
     /// channels attached to an underlying channel. This allows the channel to wake up any waiting
     /// channels by calling `thread::unpark` on all the threads it knows about.
@@ -228,23 +235,41 @@ impl ChannelMapping {
     /// operations, and the underlying [`Channel`] may become orphaned.
     pub fn remove_reference(&self, reference: Handle) -> Result<(), OakStatus> {
         if let Ok(channel_id) = self.get_writer_channel(reference) {
-            self.with_channel(channel_id, |channel| {
+            {
+                let mut channels = self.channels.write().unwrap();
+                let channel = channels
+                    .get(&channel_id)
+                    .expect("remove_reference: Handle is invalid!");
                 channel.remove_writer();
-                Ok(())
-            })?;
+                if channel.has_no_reference() {
+                    channels.remove(&channel_id);
+                    debug!("remove_reference: deallocating channel {:?}", channel_id);
+                }
+            }
 
-            let mut writers = self.writers.write().unwrap();
-            writers.remove(&reference);
+            {
+                let mut writers = self.writers.write().unwrap();
+                writers.remove(&reference);
+            }
         }
 
         if let Ok(channel_id) = self.get_reader_channel(reference) {
-            self.with_channel(channel_id, |channel| {
+            {
+                let mut channels = self.channels.write().unwrap();
+                let channel = channels
+                    .get(&channel_id)
+                    .expect("remove_reference: Handle is invalid!");
                 channel.remove_reader();
-                Ok(())
-            })?;
+                if channel.has_no_reference() {
+                    channels.remove(&channel_id);
+                    debug!("remove_reference: deallocating channel {:?}", channel_id);
+                }
+            }
 
-            let mut readers = self.readers.write().unwrap();
-            readers.remove(&reference);
+            {
+                let mut readers = self.readers.write().unwrap();
+                readers.remove(&reference);
+            }
         }
 
         Ok(())
diff --git a/oak/server/rust/oak_runtime/src/runtime/mod.rs b/oak/server/rust/oak_runtime/src/runtime/mod.rs
index 8faa94c2cec..10112f5f327 100644
--- a/oak/server/rust/oak_runtime/src/runtime/mod.rs
+++ b/oak/server/rust/oak_runtime/src/runtime/mod.rs
@@ -559,6 +559,15 @@ impl Runtime {
     /// Close a [`Handle`], potentially orphaning the underlying [`channel::Channel`].
     pub fn channel_close(&self, node_id: NodeId, reference: Handle) -> Result<(), OakStatus> {
         self.validate_handle_access(node_id, reference)?;
+
+        if node_id != RUNTIME_NODE_ID {
+            // Remove handle from the nodes available handles
+            let nodes = self.nodes.read().unwrap();
+            let node = nodes.get(&node_id).expect("channel_close: No such node_id");
+            let mut handles = node.handles.lock().unwrap();
+            handles.remove(&reference);
+        }
+
         self.channels.remove_reference(reference)
     }
 
@@ -569,8 +578,32 @@ impl Runtime {
 
     /// Remove a [`Node`] by [`NodeId`] from the [`Runtime`].
     pub fn remove_node_id(&self, node_id: NodeId) {
+        {
+            // Close any remaining handles
+            let remaining_handles: Vec<_> = {
+                let nodes = self.nodes.read().unwrap();
+                let node = nodes
+                    .get(&node_id)
+                    .expect("remove_node_id: No such node_id");
+                let handles = node.handles.lock().unwrap();
+                handles.iter().copied().collect()
+            };
+
+            debug!(
+                "remove_node_id: node_id {:?} had open channels on exit: {:?}",
+                node_id, remaining_handles
+            );
+
+            for handle in remaining_handles {
+                self.channel_close(node_id, handle)
+                    .expect("remove_node_id: Unable to close hanging channel!");
+            }
+        }
+
         let mut nodes = self.nodes.write().unwrap();
-        nodes.remove(&node_id);
+        nodes
+            .remove(&node_id)
+            .expect("remove_node_id: Node didn't exist!");
     }
 }