diff --git a/src/tabs/tab.rs b/src/tabs/tab.rs
index 89c71288..91821c42 100644
--- a/src/tabs/tab.rs
+++ b/src/tabs/tab.rs
@@ -83,19 +83,65 @@ where
     pub fn clean_tabs<F: FnMut(&mut T) -> bool>(&self, mut f: F) {
         let mut i = 0;
         let mut state = self.state.lock();
+
+        let focused_id = state.find_active_focused().map(|(_, tab)| tab.id());
+        let mut active_tab = None;
+
         loop {
             let Some(surface) = state.get_surface_mut(egui_dock::SurfaceIndex(i)) else {
                 break;
             };
+
             if let Some(tree) = surface.node_tree_mut() {
-                for node in tree.iter_mut() {
+                let mut is_empty = !egui_dock::SurfaceIndex(i).is_main();
+
+                for (j, node) in tree.iter_mut().enumerate() {
                     if let egui_dock::Node::Leaf { tabs, .. } = node {
                         tabs.retain_mut(&mut f);
+
+                        if !tabs.is_empty() {
+                            is_empty = false;
+                        }
+
+                        // Check if the originally focused tab is inside this tree
+                        if let Some(k) = focused_id.and_then(|id| {
+                            tabs.iter().enumerate().find_map(|(i, tab)| {
+                                if tab.id() == id {
+                                    Some(i)
+                                } else {
+                                    None
+                                }
+                            })
+                        }) {
+                            active_tab = Some((i, j, k));
+                        }
                     }
                 }
+
+                // We need to remove empty windows or we'll cause a crash
+                if is_empty {
+                    state.remove_surface(egui_dock::SurfaceIndex(i));
+                }
             }
             i += 1;
         }
+
+        // If the previously focused tab hasn't been removed, refocus it since the index may have
+        // changed, otherwise the application may crash due to out-of-bounds vector access
+        if let Some((i, j, k)) = active_tab {
+            state.set_active_tab((
+                egui_dock::SurfaceIndex(i),
+                egui_dock::NodeIndex(j),
+                egui_dock::TabIndex(k),
+            ));
+        }
+        // Otherwise we need to unfocus all tabs, again to prevent a crash
+        else {
+            state.set_focused_node_and_surface((
+                egui_dock::SurfaceIndex(usize::MAX),
+                egui_dock::NodeIndex(usize::MAX),
+            ));
+        }
     }
 
     /// Returns the name of the focused tab.