diff --git a/crates/goose/src/context_mgmt/auto_compact.rs b/crates/goose/src/context_mgmt/auto_compact.rs
index aebd1096e25a..542d252f3108 100644
--- a/crates/goose/src/context_mgmt/auto_compact.rs
+++ b/crates/goose/src/context_mgmt/auto_compact.rs
@@ -167,8 +167,7 @@ pub async fn perform_compaction(agent: &Agent, messages: &[Message]) -> Result<A
 /// Check if messages need compaction and compact them if necessary
 ///
 /// This is a convenience wrapper function that combines checking and compaction.
-/// If the most recent message is a user message, it will be preserved by removing it
-/// before compaction and adding it back afterwards.
+/// Uses perform_compaction internally to handle the actual compaction process.
 ///
 /// # Arguments
 /// * `agent` - The agent to use for context management
@@ -207,35 +206,7 @@ pub async fn check_and_compact_messages(
         check_result.usage_ratio * 100.0
     );
 
-    // Check if the most recent message is a user message
-    let (messages_to_compact, preserved_user_message) = if let Some(last_message) = messages.last()
-    {
-        if matches!(last_message.role, rmcp::model::Role::User) {
-            // Remove the last user message before auto-compaction
-            (&messages[..messages.len() - 1], Some(last_message.clone()))
-        } else {
-            (messages, None)
-        }
-    } else {
-        (messages, None)
-    };
-
-    // Perform the compaction on messages excluding the preserved user message
-    // The summarize_context method already handles the visibility properly
-    let (mut summary_messages, _, summarization_usage) =
-        agent.summarize_context(messages_to_compact).await?;
-
-    // Add back the preserved user message if it exists
-    // (keeps default visibility: both true)
-    if let Some(user_message) = preserved_user_message {
-        summary_messages.push(user_message);
-    }
-
-    Ok(AutoCompactResult {
-        compacted: true,
-        messages: summary_messages,
-        summarization_usage,
-    })
+    perform_compaction(agent, messages).await
 }
 
 #[cfg(test)]
diff --git a/crates/goose/src/conversation/mod.rs b/crates/goose/src/conversation/mod.rs
index a77442b075d4..bb9f673fecaa 100644
--- a/crates/goose/src/conversation/mod.rs
+++ b/crates/goose/src/conversation/mod.rs
@@ -161,10 +161,35 @@ impl<'a> IntoIterator for &'a Conversation {
 
 /// Fix a conversation that we're about to send to an LLM. So the last and first
 /// messages should always be from the user.
+///
+/// This function handles agent_visible and non-visible messages separately to ensure
+/// that only agent-visible messages are fixed, while preserving non-visible messages.
 pub fn fix_conversation(conversation: Conversation) -> (Conversation, Vec<String>) {
-    let messages = conversation.messages().clone();
-    let (messages, issues) = fix_messages(messages);
-    (Conversation::new_unvalidated(messages), issues)
+    let all_messages = conversation.messages().clone();
+
+    // Separate agent-visible and non-visible messages
+    let mut agent_visible_messages = Vec::new();
+    let mut non_visible_messages = Vec::new();
+
+    for msg in all_messages {
+        if msg.metadata.agent_visible {
+            agent_visible_messages.push(msg);
+        } else {
+            non_visible_messages.push(msg);
+        }
+    }
+
+    // Only fix agent-visible messages
+    let (fixed_visible, issues) = fix_messages(agent_visible_messages);
+
+    // Combine back: non-visible messages stay unchanged, visible messages are fixed
+    let mut final_messages = non_visible_messages;
+    final_messages.extend(fixed_visible);
+
+    // Sort by timestamp to maintain order
+    final_messages.sort_by_key(|m| m.created);
+
+    (Conversation::new_unvalidated(final_messages), issues)
 }
 
 fn fix_messages(messages: Vec<Message>) -> (Vec<Message>, Vec<String>) {
@@ -389,7 +414,8 @@ fn fix_lead_trail(mut messages: Vec<Message>) -> (Vec<Message>, Vec<String>) {
     if let Some(last) = messages.last() {
         if last.role == Role::Assistant {
             messages.pop();
-            issues.push("Removed trailing assistant message".to_string());
+            issues
+                .push("Removed trailing assistant message with pending tool requests".to_string());
         }
     }
 
@@ -752,4 +778,85 @@ mod tests {
             panic!("Expected second item to be an image");
         }
     }
+
+    #[test]
+    fn test_last_assistant_message_with_pending_tool_request() {
+        // Test the scenario where the last assistant message has a tool request
+        // This should be removed to prevent orphaned tool responses after compaction
+        let messages = vec![
+            Message::user().with_text("Help me with something"),
+            Message::assistant()
+                .with_text("I'll help you with that")
+                .with_tool_request(
+                    "tool_1",
+                    Ok(CallToolRequestParam {
+                        name: "some_tool".into(),
+                        arguments: Some(object!({})),
+                    }),
+                ),
+        ];
+
+        let (fixed, issues) = run_verify(messages);
+
+        // The entire last assistant message should be removed
+        assert_eq!(fixed.len(), 1);
+        assert_eq!(issues.len(), 2);
+
+        // Should have removed the orphaned tool request and the trailing assistant message
+        assert!(issues
+            .iter()
+            .any(|i| i.contains("Removed orphaned tool request 'tool_1'")));
+        assert!(issues
+            .iter()
+            .any(|i| i.contains("Removed trailing assistant message")));
+
+        // Only the user message should remain
+        assert_eq!(fixed[0].role, Role::User);
+        assert!(fixed[0].as_concat_text().contains("Help me with something"));
+    }
+
+    #[test]
+    fn test_last_assistant_message_with_multiple_pending_tool_requests() {
+        // Test with multiple tool requests in the last assistant message
+        let messages = vec![
+            Message::user().with_text("Do multiple things"),
+            Message::assistant()
+                .with_text("I'll do multiple things")
+                .with_tool_request(
+                    "tool_1",
+                    Ok(CallToolRequestParam {
+                        name: "tool_a".into(),
+                        arguments: Some(object!({})),
+                    }),
+                )
+                .with_tool_request(
+                    "tool_2",
+                    Ok(CallToolRequestParam {
+                        name: "tool_b".into(),
+                        arguments: Some(object!({})),
+                    }),
+                ),
+        ];
+
+        let (fixed, issues) = run_verify(messages);
+
+        // The entire last assistant message should be removed
+        assert_eq!(fixed.len(), 1);
+        assert_eq!(issues.len(), 3);
+
+        // Should have removed both orphaned tool requests and the trailing assistant message
+        assert!(issues
+            .iter()
+            .any(|i| i.contains("Removed orphaned tool request 'tool_1'")));
+        assert!(issues
+            .iter()
+            .any(|i| i.contains("Removed orphaned tool request 'tool_2'")));
+        assert!(issues
+            .iter()
+            .any(|i| i.contains("Removed trailing assistant message")));
+
+        // Only the user message should remain
+        assert_eq!(fixed[0].role, Role::User);
+        assert!(fixed[0].as_concat_text().contains("Do multiple things"));
+    }
 }