diff --git a/src/mcp/mod.rs b/src/mcp/mod.rs
index 492eeba..5213bcd 100644
--- a/src/mcp/mod.rs
+++ b/src/mcp/mod.rs
@@ -158,27 +158,31 @@ impl McpRegistry {
     }
 
     pub async fn reinit(
-        registry: McpRegistry,
+        mut registry: McpRegistry,
         enabled_mcp_servers: Option<String>,
         abort_signal: AbortSignal,
     ) -> Result<Self> {
         debug!("Reinitializing MCP registry");
-        debug!("Stopping all MCP servers");
-        let mut new_registry = abortable_run_with_spinner(
-            registry.stop_all_servers(),
-            "Stopping MCP servers",
+
+        let desired_ids = registry.resolve_server_ids(enabled_mcp_servers.clone());
+        let desired_set: HashSet<String> = desired_ids.iter().cloned().collect();
+
+        debug!("Stopping unused MCP servers");
+        abortable_run_with_spinner(
+            registry.stop_unused_servers(&desired_set),
+            "Stopping unused MCP servers",
             abort_signal.clone(),
         )
         .await?;
 
         abortable_run_with_spinner(
-            new_registry.start_select_mcp_servers(enabled_mcp_servers),
+            registry.start_select_mcp_servers(enabled_mcp_servers),
             "Loading MCP servers",
             abort_signal,
         )
         .await?;
 
-        Ok(new_registry)
+        Ok(registry)
     }
 
     async fn start_select_mcp_servers(
@@ -192,43 +196,29 @@ impl McpRegistry {
             return Ok(());
         }
 
-        if let Some(servers) = enabled_mcp_servers {
-            debug!("Starting selected MCP servers: {:?}", servers);
-            let config = self
-                .config
-                .as_ref()
-                .with_context(|| "MCP Config not defined. Cannot start servers")?;
-            let mcp_servers = config.mcp_servers.clone();
+        let desired_ids = self.resolve_server_ids(enabled_mcp_servers);
+        let ids_to_start: Vec<String> = desired_ids.into_iter()
+            .filter(|id| !self.servers.contains_key(id))
+            .collect();
 
-            let enabled_servers: HashSet<String> =
-                servers.split(',').map(|s| s.trim().to_string()).collect();
-            let server_ids: Vec<String> = if servers == "all" {
-                mcp_servers.into_keys().collect()
-            } else {
-                mcp_servers
-                    .into_keys()
-                    .filter(|id| enabled_servers.contains(id))
-                    .collect()
-            };
+        if ids_to_start.is_empty() {
+            return Ok(());
+        }
 
-            let results: Vec<(String, Arc<_>, ServerCatalog)> = stream::iter(
-                server_ids
-                    .into_iter()
-                    .map(|id| async { self.start_server(id).await }),
-            )
-            .buffer_unordered(num_cpus::get())
-            .try_collect()
-            .await?;
+        debug!("Starting selected MCP servers: {:?}", ids_to_start);
 
-            self.servers = results
-                .clone()
+        let results: Vec<(String, Arc<_>, ServerCatalog)> = stream::iter(
+            ids_to_start
                 .into_iter()
-                .map(|(id, server, _)| (id, server))
-                .collect();
-            self.catalogs = results
-                .into_iter()
-                .map(|(id, _, catalog)| (id, catalog))
-                .collect();
+                .map(|id| async { self.start_server(id).await }),
+        )
+        .buffer_unordered(num_cpus::get())
+        .try_collect()
+        .await?;
+
+        for (id, server, catalog) in results {
+            self.servers.insert(id.clone(), server);
+            self.catalogs.insert(id, catalog);
         }
 
         Ok(())
@@ -309,19 +299,49 @@ impl McpRegistry {
         Ok((id.to_string(), service, catalog))
     }
 
-    pub async fn stop_all_servers(mut self) -> Result<Self> {
-        for (id, server) in self.servers {
-            Arc::try_unwrap(server)
-                .map_err(|_| anyhow!("Failed to unwrap Arc for MCP server: {id}"))?
-                .cancel()
-                .await
-                .with_context(|| format!("Failed to stop MCP server: {id}"))?;
-            info!("Stopped MCP server: {id}");
+    fn resolve_server_ids(&self, enabled_mcp_servers: Option<String>) -> Vec<String> {
+        if let Some(config) = &self.config
+             && let Some(servers) = enabled_mcp_servers {
+                if servers == "all" {
+                    config.mcp_servers.keys().cloned().collect()
+                } else {
+                    let enabled_servers: HashSet<String> =
+                        servers.split(',').map(|s| s.trim().to_string()).collect();
+                    config.mcp_servers
+                        .keys()
+                        .filter(|id| enabled_servers.contains(*id))
+                        .cloned()
+                        .collect()
+                }
+        } else {
+            vec![]
+        }
+    }
+
+    pub async fn stop_unused_servers(&mut self, keep_ids: &HashSet<String>) -> Result<()> {
+        let mut ids_to_remove = Vec::new();
+        for (id, _) in self.servers.iter() {
+            if !keep_ids.contains(id) {
+                ids_to_remove.push(id.clone());
+            }
         }
 
-        self.servers = HashMap::new();
-
-        Ok(self)
+        for id in ids_to_remove {
+            if let Some(server) = self.servers.remove(&id) {
+                match Arc::try_unwrap(server) {
+                    Ok(server_inner) => {
+                        server_inner.cancel().await
+                            .with_context(|| format!("Failed to stop MCP server: {id}"))?;
+                        info!("Stopped MCP server: {id}");
+                    }
+                    Err(_) => {
+                        info!("Detaching from MCP server: {id} (still in use)");
+                    }
+                }
+                self.catalogs.remove(&id);
+            }
+        }
+        Ok(())
     }
 
     pub fn list_started_servers(&self) -> Vec<String> {