diff --git a/src/auto_splitting/mod.rs b/src/auto_splitting/mod.rs
index 918c486b..2d2fa2a8 100644
--- a/src/auto_splitting/mod.rs
+++ b/src/auto_splitting/mod.rs
@@ -543,7 +543,7 @@
 
 use crate::{
     platform::Arc,
-    timing::{SharedTimer, TimerPhase},
+    timing::{self, SharedTimer, TimerPhase},
 };
 pub use livesplit_auto_splitting::{settings, wasi_path};
 use livesplit_auto_splitting::{
@@ -665,8 +665,9 @@ impl Runtime {
         compiled_auto_splitter: &CompiledAutoSplitter,
         timer: SharedTimer,
     ) -> Result<(), Error> {
+        let settings_map = get_timer_auto_splitter_settings(&timer);
         let auto_splitter = compiled_auto_splitter
-            .instantiate(Timer(timer), None, None)
+            .instantiate(Timer(timer), settings_map, None)
             .map_err(|e| Error::LoadFailed { source: e })?;
 
         self.auto_splitter
@@ -674,6 +675,18 @@ impl Runtime {
             .map_err(|_| Error::ThreadStopped)
     }
 
+    /// Update's the timer's run's auto splitter settings from the Runtime.
+    /// Call this before saving a timer into a splits file.
+    pub fn update_timer_auto_splitter_settings(&self, timer: &mut timing::Timer) {
+        let Some(settings_map) = self.settings_map() else {
+            return;
+        };
+        if timer.run().parsed_auto_splitter_settings().is_none() && settings_map.is_empty() {
+            return;
+        }
+        timer.set_auto_splitter_settings_map(settings_map);
+    }
+
     /// Unloads the current auto splitter. This will _not_ return an error if
     /// there isn't currently an auto splitter loaded, only if the runtime
     /// thread stops unexpectedly.
@@ -889,3 +902,13 @@ async fn watchdog(
         }
     }
 }
+
+/// Gets the timer's run's auto splitter settings to instantiate with.
+fn get_timer_auto_splitter_settings(timer: &SharedTimer) -> Option<settings::Map> {
+    let t = timer.read().ok()?;
+    let run = t.run();
+    if let Some(p) = run.parsed_auto_splitter_settings() {
+        return Some(p.custom_settings.clone());
+    }
+    None
+}
diff --git a/src/run/mod.rs b/src/run/mod.rs
index 3d258e30..f028e6ae 100644
--- a/src/run/mod.rs
+++ b/src/run/mod.rs
@@ -340,6 +340,25 @@ impl Run {
         &mut self.parsed_auto_splitter_settings
     }
 
+    /// Set the settings map in the parsed auto splitter settings.
+    #[cfg(feature = "auto-splitting")]
+    pub fn set_auto_splitter_settings_map(
+        &mut self,
+        settings_map: livesplit_auto_splitting::settings::Map,
+    ) {
+        let p = self.parsed_auto_splitter_settings_mut();
+        match p {
+            None => {
+                let mut a = AutoSplitterSettings::default();
+                a.set_custom_settings(settings_map);
+                *p = Some(a);
+            }
+            Some(a) => {
+                a.set_custom_settings(settings_map);
+            }
+        }
+    }
+
     /// Accesses the [`LinkedLayout`] of this `Run`. If a
     /// [`Layout`](crate::Layout) is linked, it is supposed to be loaded to
     /// visualize the `Run`.
diff --git a/src/timing/timer/mod.rs b/src/timing/timer/mod.rs
index 7da2bfe2..ef46019f 100644
--- a/src/timing/timer/mod.rs
+++ b/src/timing/timer/mod.rs
@@ -180,6 +180,15 @@ impl Timer {
         &self.run
     }
 
+    /// Set the settings map in the parsed auto splitter settings.
+    #[cfg(feature = "auto-splitting")]
+    pub fn set_auto_splitter_settings_map(
+        &mut self,
+        settings_map: livesplit_auto_splitting::settings::Map,
+    ) {
+        self.run.set_auto_splitter_settings_map(settings_map);
+    }
+
     /// Marks the Run as unmodified, so that it is known that all the changes
     /// have been saved.
     #[inline]