diff --git a/src/backend/mod.rs b/src/backend/mod.rs
index 710b91ba..caba2d44 100644
--- a/src/backend/mod.rs
+++ b/src/backend/mod.rs
@@ -65,6 +65,15 @@ pub fn init_backend_auto(
             .unwrap()
             .seats
             .add_seat(initial_seat);
+
+        {
+            {
+                let (lock, cvar) = &*state.common.startup_done;
+                let mut startup = lock.lock().unwrap();
+                *startup = true;
+                cvar.notify_all();
+            }
+        }
     }
     res
 }
diff --git a/src/backend/winit.rs b/src/backend/winit.rs
index d1025876..646b8d89 100644
--- a/src/backend/winit.rs
+++ b/src/backend/winit.rs
@@ -107,15 +107,15 @@ impl WinitState {
         Ok(())
     }
 
-    pub fn apply_config_for_output(
+    pub fn apply_config_for_outputs(
         &mut self,
-        output: &Output,
         test_only: bool,
-    ) -> Result<(), anyhow::Error> {
+    ) -> Result<Vec<Output>, anyhow::Error> {
         // TODO: if we ever have multiple winit outputs, don't ignore config.enabled
         // reset size
         let size = self.backend.window_size();
-        let mut config = output
+        let mut config = self
+            .output
             .user_data()
             .get::<RefCell<OutputConfig>>()
             .unwrap()
@@ -126,7 +126,7 @@ impl WinitState {
             }
             Err(anyhow::anyhow!("Cannot set window size"))
         } else {
-            Ok(())
+            Ok(vec![self.output.clone()])
         }
     }
 }
@@ -229,17 +229,15 @@ pub fn init_backend(
         .add_heads(std::iter::once(&output));
     {
         state.common.add_output(&output);
-        let mut shell = state.common.shell.write().unwrap();
         state.common.config.read_outputs(
             &mut state.common.output_configuration_state,
             &mut state.backend,
-            &mut *shell,
+            &state.common.shell,
             &state.common.event_loop_handle,
             &mut state.common.workspace_state.update(),
             &state.common.xdg_activation_state,
+            state.common.startup_done.clone(),
         );
-
-        std::mem::drop(shell);
         state.common.refresh();
     }
     state.launch_xwayland(None);
diff --git a/src/backend/x11.rs b/src/backend/x11.rs
index 97db92be..7bf27077 100644
--- a/src/backend/x11.rs
+++ b/src/backend/x11.rs
@@ -167,32 +167,29 @@ impl X11State {
         }
     }
 
-    pub fn apply_config_for_output(
+    pub fn apply_config_for_outputs(
         &mut self,
-        output: &Output,
         test_only: bool,
-    ) -> Result<(), anyhow::Error> {
-        // TODO: if we ever have multiple winit outputs, don't ignore config.enabled
-        // reset size
-        let size = self
-            .surfaces
-            .iter()
-            .find(|s| s.output == *output)
-            .unwrap()
-            .window
-            .size();
-        let mut config = output
+    ) -> Result<Vec<Output>, anyhow::Error> {
+        // TODO: if we ever have multiple winit outputs, don't juse use the first and don't ignore OutputState
+
+        let surface = self.surfaces.first().unwrap();
+        let size = surface.window.size();
+        let mut config = surface
+            .output
             .user_data()
             .get::<RefCell<OutputConfig>>()
             .unwrap()
             .borrow_mut();
+
+        // reset size
         if config.mode.0 != (size.w as i32, size.h as i32) {
             if !test_only {
                 config.mode = ((size.w as i32, size.h as i32), None);
             }
             Err(anyhow::anyhow!("Cannot set window size"))
         } else {
-            Ok(())
+            Ok(vec![surface.output.clone()])
         }
     }
 }
@@ -366,17 +363,15 @@ pub fn init_backend(
         .add_heads(std::iter::once(&output));
     {
         state.common.add_output(&output);
-        let mut shell = state.common.shell.write().unwrap();
         state.common.config.read_outputs(
             &mut state.common.output_configuration_state,
             &mut state.backend,
-            &mut *shell,
+            &state.common.shell,
             &state.common.event_loop_handle,
             &mut state.common.workspace_state.update(),
             &state.common.xdg_activation_state,
+            state.common.startup_done.clone(),
         );
-
-        std::mem::drop(shell);
         state.common.refresh();
     }
     state.launch_xwayland(None);
diff --git a/src/config/mod.rs b/src/config/mod.rs
index 9f3ea3c5..c4352e77 100644
--- a/src/config/mod.rs
+++ b/src/config/mod.rs
@@ -23,7 +23,13 @@ pub use smithay::{
     },
     utils::{Logical, Physical, Point, Size, Transform},
 };
-use std::{cell::RefCell, collections::HashMap, fs::OpenOptions, path::PathBuf};
+use std::{
+    cell::RefCell,
+    collections::HashMap,
+    fs::OpenOptions,
+    path::PathBuf,
+    sync::{Arc, Condvar, Mutex, RwLock},
+};
 use tracing::{debug, error, info, warn};
 
 mod input_config;
@@ -312,10 +318,11 @@ impl Config {
         &mut self,
         output_state: &mut OutputConfigurationState<State>,
         backend: &mut BackendData,
-        shell: &mut Shell,
-        loop_handle: &LoopHandle<'_, State>,
+        shell: &Arc<RwLock<Shell>>,
+        loop_handle: &LoopHandle<'static, State>,
         workspace_state: &mut WorkspaceUpdateGuard<'_, State>,
         xdg_activation_state: &XdgActivationState,
+        startup_done: Arc<(Mutex<bool>, Condvar)>,
     ) {
         let outputs = output_state.outputs().collect::<Vec<_>>();
         let mut infos = outputs
@@ -325,7 +332,6 @@ impl Config {
             .collect::<Vec<_>>();
         infos.sort();
         if let Some(configs) = self.dynamic_conf.outputs().config.get(&infos).cloned() {
-            let mut reset = false;
             let known_good_configs = outputs
                 .iter()
                 .map(|output| {
@@ -338,6 +344,7 @@ impl Config {
                 })
                 .collect::<Vec<_>>();
 
+            let mut found_outputs = Vec::new();
             for (name, output_config) in infos.iter().map(|o| &o.connector).zip(configs.into_iter())
             {
                 let output = outputs.iter().find(|o| &o.name() == name).unwrap().clone();
@@ -347,31 +354,19 @@ impl Config {
                     .get::<RefCell<OutputConfig>>()
                     .unwrap()
                     .borrow_mut() = output_config;
-                if let Err(err) = backend.apply_config_for_output(
-                    &output,
-                    false,
-                    shell,
-                    loop_handle,
-                    workspace_state,
-                    xdg_activation_state,
-                ) {
-                    warn!(
-                        ?err,
-                        "Failed to set new config for output {}.",
-                        output.name(),
-                    );
-                    reset = true;
-                    break;
-                } else {
-                    if enabled == OutputState::Enabled {
-                        output_state.enable_head(&output);
-                    } else {
-                        output_state.disable_head(&output);
-                    }
-                }
+                found_outputs.push((output.clone(), enabled));
             }
 
-            if reset {
+            if let Err(err) = backend.apply_config_for_outputs(
+                false,
+                loop_handle,
+                shell.clone(),
+                workspace_state,
+                xdg_activation_state,
+                startup_done.clone(),
+            ) {
+                warn!(?err, "Failed to set new config.");
+                found_outputs.clear();
                 for (output, output_config) in outputs
                     .clone()
                     .into_iter()
@@ -383,16 +378,20 @@ impl Config {
                         .get::<RefCell<OutputConfig>>()
                         .unwrap()
                         .borrow_mut() = output_config;
-                    if let Err(err) = backend.apply_config_for_output(
-                        &output,
-                        false,
-                        shell,
-                        loop_handle,
-                        workspace_state,
-                        xdg_activation_state,
-                    ) {
-                        error!(?err, "Failed to reset config for output {}.", output.name());
-                    } else {
+                    found_outputs.push((output.clone(), enabled));
+                }
+
+                if let Err(err) = backend.apply_config_for_outputs(
+                    false,
+                    loop_handle,
+                    shell.clone(),
+                    workspace_state,
+                    xdg_activation_state,
+                    startup_done,
+                ) {
+                    error!(?err, "Failed to reset config.");
+                } else {
+                    for (output, enabled) in found_outputs {
                         if enabled == OutputState::Enabled {
                             output_state.enable_head(&output);
                         } else {
@@ -400,26 +399,30 @@ impl Config {
                         }
                     }
                 }
+            } else {
+                for (output, enabled) in found_outputs {
+                    if enabled == OutputState::Enabled {
+                        output_state.enable_head(&output);
+                    } else {
+                        output_state.disable_head(&output);
+                    }
+                }
             }
 
             output_state.update();
             self.write_outputs(output_state.outputs());
         } else {
-            for output in outputs {
-                if let Err(err) = backend.apply_config_for_output(
-                    &output,
-                    false,
-                    shell,
-                    loop_handle,
-                    workspace_state,
-                    xdg_activation_state,
-                ) {
-                    warn!(
-                        ?err,
-                        "Failed to set new config for output {}.",
-                        output.name(),
-                    );
-                } else {
+            if let Err(err) = backend.apply_config_for_outputs(
+                false,
+                loop_handle,
+                shell.clone(),
+                workspace_state,
+                xdg_activation_state,
+                startup_done,
+            ) {
+                warn!(?err, "Failed to set new config.",);
+            } else {
+                for output in outputs {
                     if output
                         .user_data()
                         .get::<RefCell<OutputConfig>>()
diff --git a/src/state.rs b/src/state.rs
index 2d4ac8e4..258de36c 100644
--- a/src/state.rs
+++ b/src/state.rs
@@ -106,7 +106,7 @@ use std::{
     collections::{HashSet, VecDeque},
     ffi::OsString,
     process::Child,
-    sync::{Arc, Once, RwLock},
+    sync::{Arc, Condvar, Mutex, Once, RwLock},
     time::{Duration, Instant},
 };
 
@@ -179,6 +179,7 @@ pub struct Common {
     pub shell: Arc<RwLock<Shell>>,
 
     pub clock: Clock<Monotonic>,
+    pub startup_done: Arc<(Mutex<bool>, Condvar)>,
     pub should_stop: bool,
     pub local_offset: time::UtcOffset,
     pub gesture_state: Option<GestureState>,
@@ -262,30 +263,26 @@ impl BackendData {
         }
     }
 
-    pub fn apply_config_for_output(
+    pub fn apply_config_for_outputs(
         &mut self,
-        output: &Output,
         test_only: bool,
-        shell: &mut Shell,
-        loop_handle: &LoopHandle<'_, State>,
+        loop_handle: &LoopHandle<'static, State>,
+        shell: Arc<RwLock<Shell>>,
         workspace_state: &mut WorkspaceUpdateGuard<'_, State>,
         xdg_activation_state: &XdgActivationState,
+        startup_done: Arc<(Mutex<bool>, Condvar)>,
     ) -> Result<(), anyhow::Error> {
         let result = match self {
-            BackendData::Kms(ref mut state) => state.apply_config_for_output(
-                output,
-                shell,
-                test_only,
-                loop_handle,
-                workspace_state,
-                xdg_activation_state,
-            ),
-            BackendData::Winit(ref mut state) => state.apply_config_for_output(output, test_only),
-            BackendData::X11(ref mut state) => state.apply_config_for_output(output, test_only),
+            BackendData::Kms(ref mut state) => {
+                state.apply_config_for_outputs(test_only, loop_handle, shell.clone(), startup_done)
+            }
+            BackendData::Winit(ref mut state) => state.apply_config_for_outputs(test_only),
+            BackendData::X11(ref mut state) => state.apply_config_for_outputs(test_only),
             _ => unreachable!("No backend set when applying output config"),
-        };
+        }?;
 
-        if result.is_ok() {
+        let mut shell = shell.write().unwrap();
+        for output in result {
             // apply to Output
             let final_config = output
                 .user_data()
@@ -318,10 +315,29 @@ impl BackendData {
                 _ => None,
             });
 
-            layer_map_for_output(output).arrange();
+            match final_config.enabled {
+                OutputState::Enabled => {
+                    shell
+                        .workspaces
+                        .add_output(&output, workspace_state, xdg_activation_state)
+                }
+                _ => {
+                    let shell = &mut *shell;
+                    shell.workspaces.remove_output(
+                        &output,
+                        shell.seats.iter(),
+                        workspace_state,
+                        xdg_activation_state,
+                    )
+                }
+            }
+
+            layer_map_for_output(&output).arrange();
+
+            self.schedule_render(loop_handle, &output);
         }
 
-        result
+        Ok(())
     }
 
     pub fn schedule_render(&mut self, loop_handle: &LoopHandle<'_, State>, output: &Output) {
@@ -494,6 +510,7 @@ impl State {
                 local_offset,
 
                 clock,
+                startup_done: Arc::new((Mutex::new(false), Condvar::new())),
                 should_stop: false,
                 gesture_state: None,
 
diff --git a/src/utils/prelude.rs b/src/utils/prelude.rs
index dd3fe8e7..39d71a7e 100644
--- a/src/utils/prelude.rs
+++ b/src/utils/prelude.rs
@@ -4,13 +4,17 @@ use smithay::{
 };
 
 pub use super::geometry::*;
+use crate::config::{OutputConfig, OutputState};
 pub use crate::shell::{SeatExt, Shell, Workspace};
 pub use crate::state::{Common, State};
 pub use crate::wayland::handlers::xdg_shell::popup::update_reactive_popups;
 
-use std::sync::{
-    atomic::{AtomicBool, Ordering},
-    Mutex,
+use std::{
+    cell::{Ref, RefCell, RefMut},
+    sync::{
+        atomic::{AtomicBool, Ordering},
+        Mutex,
+    },
 };
 
 pub trait OutputExt {
@@ -19,6 +23,10 @@ pub trait OutputExt {
     fn set_adaptive_sync(&self, vrr: bool);
     fn mirroring(&self) -> Option<Output>;
     fn set_mirroring(&self, output: Option<Output>);
+
+    fn is_enabled(&self) -> bool;
+    fn config(&self) -> Ref<'_, OutputConfig>;
+    fn config_mut(&self) -> RefMut<'_, OutputConfig>;
 }
 
 struct Vrr(AtomicBool);
@@ -73,4 +81,25 @@ impl OutputExt for Output {
         *user_data.get::<Mirroring>().unwrap().0.lock().unwrap() =
             output.map(|output| output.downgrade());
     }
+
+    fn is_enabled(&self) -> bool {
+        self.user_data()
+            .get::<RefCell<OutputConfig>>()
+            .map(|conf| conf.borrow().enabled != OutputState::Disabled)
+            .unwrap_or(false)
+    }
+
+    fn config(&self) -> Ref<'_, OutputConfig> {
+        self.user_data()
+            .get::<RefCell<OutputConfig>>()
+            .unwrap()
+            .borrow()
+    }
+
+    fn config_mut(&self) -> RefMut<'_, OutputConfig> {
+        self.user_data()
+            .get::<RefCell<OutputConfig>>()
+            .unwrap()
+            .borrow_mut()
+    }
 }
diff --git a/src/wayland/handlers/output_configuration.rs b/src/wayland/handlers/output_configuration.rs
index f0f5b280..4b5993b3 100644
--- a/src/wayland/handlers/output_configuration.rs
+++ b/src/wayland/handlers/output_configuration.rs
@@ -90,51 +90,44 @@ impl State {
                     current_config.enabled = OutputState::Disabled;
                 }
             }
-
-            let mut shell = self.common.shell.write().unwrap();
-            let res = self.backend.apply_config_for_output(
-                output,
-                test_only,
-                &mut *shell,
-                &self.common.event_loop_handle,
-                &mut self.common.workspace_state.update(),
-                &self.common.xdg_activation_state,
-            );
-            if let Err(err) = res {
-                warn!(
-                    ?err,
-                    "Failed to apply config to {}. Resetting",
-                    output.name(),
-                );
-                for (output, backup) in backups {
-                    {
-                        let mut current_config = output
-                            .user_data()
-                            .get::<RefCell<OutputConfig>>()
-                            .unwrap()
-                            .borrow_mut();
-                        *current_config = backup;
-                    }
-                    if !test_only {
-                        if let Err(err) = self.backend.apply_config_for_output(
-                            output,
-                            false,
-                            &mut *shell,
-                            &self.common.event_loop_handle,
-                            &mut self.common.workspace_state.update(),
-                            &self.common.xdg_activation_state,
-                        ) {
-                            error!(?err, "Failed to reset output config for {}.", output.name(),);
-                        }
-                    }
-                }
-                return false;
-            }
-
-            std::mem::drop(shell);
-            self.common.refresh();
         }
 
+        let res = self.backend.apply_config_for_outputs(
+            test_only,
+            &self.common.event_loop_handle,
+            self.common.shell.clone(),
+            &mut self.common.workspace_state.update(),
+            &self.common.xdg_activation_state,
+            self.common.startup_done.clone(),
+        );
+        if let Err(err) = res {
+            warn!(?err, "Failed to apply config. Resetting");
+            for (output, backup) in backups {
+                {
+                    let mut current_config = output
+                        .user_data()
+                        .get::<RefCell<OutputConfig>>()
+                        .unwrap()
+                        .borrow_mut();
+                    *current_config = backup;
+                }
+            }
+            if !test_only {
+                if let Err(err) = self.backend.apply_config_for_outputs(
+                    false,
+                    &self.common.event_loop_handle,
+                    self.common.shell.clone(),
+                    &mut self.common.workspace_state.update(),
+                    &self.common.xdg_activation_state,
+                    self.common.startup_done.clone(),
+                ) {
+                    error!(?err, "Failed to reset output config.");
+                }
+            }
+            return false;
+        }
+        self.common.refresh();
+
         for output in conf
             .iter()
             .filter(|(_, c)| {