diff --git a/apps/desktop/src-tauri/src/extensions.rs b/apps/desktop/src-tauri/src/extensions.rs
index e8236cdb..7b5e9e3e 100644
--- a/apps/desktop/src-tauri/src/extensions.rs
+++ b/apps/desktop/src-tauri/src/extensions.rs
@@ -527,7 +527,7 @@ pub async fn toggle_extension_state(
     }
 
     let json = serde_json::to_string_pretty(&disabled).map_err(|e| e.to_string())?;
-    std::fs::write(disabled_file, json).map_err(|e| e.to_string())?;
+    crate::fs_atomic::write_atomic(&disabled_file, json.as_bytes()).map_err(|e| e.to_string())?;
 
     Ok(())
 }
diff --git a/apps/desktop/src-tauri/src/fs_atomic.rs b/apps/desktop/src-tauri/src/fs_atomic.rs
new file mode 100644
index 00000000..6c2958a2
--- /dev/null
+++ b/apps/desktop/src-tauri/src/fs_atomic.rs
@@ -0,0 +1,223 @@
+use std::fs::OpenOptions;
+use std::io::Write;
+use std::path::Path;
+use std::sync::atomic::{AtomicU64, Ordering};
+
+/// Write `bytes` to `path` atomically: stream to a sibling temp file, fsync
+/// it, then rename over the destination.
+///
+/// On POSIX `rename` is atomic at the filesystem level. On Windows
+/// `std::fs::rename` maps to `MoveFileEx` with
+/// `MOVEFILE_REPLACE_EXISTING | MOVEFILE_WRITE_THROUGH`, which performs the
+/// replacement atomically on NTFS for same-volume targets. Either way, a
+/// crash or power loss mid-write leaves the **original** file on disk
+/// rather than a half-written truncation.
+///
+/// The temp file lives alongside the target so the rename stays on the
+/// same volume (the atomicity guarantee is per-volume). The temp name
+/// combines a process-wide atomic counter with PID and a nanosecond
+/// timestamp, and is opened with `create_new(true)` so two concurrent
+/// callers racing on the same target can never share the same file
+/// (the loser retries with a new suffix rather than sharing-and-truncating
+/// an existing temp).
+///
+/// When the destination already exists, its mode bits (on Unix) are copied
+/// onto the temp file before the rename so an executable being atomically
+/// replaced doesn't silently lose its `+x` bit. On Windows, ACLs inherited
+/// from the destination's parent directory apply to the new file; that's
+/// the same inheritance git/editors rely on for new files, so we don't
+/// attempt manual ACL copy.
+pub fn write_atomic(path: &Path, bytes: &[u8]) -> std::io::Result<()> {
+    let parent = path.parent().ok_or_else(|| {
+        std::io::Error::new(
+            std::io::ErrorKind::InvalidInput,
+            "atomic write target has no parent directory",
+        )
+    })?;
+
+    if !parent.as_os_str().is_empty() && !parent.exists() {
+        std::fs::create_dir_all(parent)?;
+    }
+
+    let file_name = path
+        .file_name()
+        .ok_or_else(|| {
+            std::io::Error::new(
+                std::io::ErrorKind::InvalidInput,
+                "atomic write target has no file name",
+            )
+        })?
+        .to_string_lossy()
+        .into_owned();
+
+    // Open a fresh temp file with create_new(true). On collision (another
+    // process / another thread inside the same process already minted the
+    // same suffix) the call errors with AlreadyExists and we loop with a
+    // new suffix rather than truncating a temp that someone else owns.
+    let (tmp_path, mut tmp) = create_unique_temp(parent, &file_name)?;
+
+    // Write + fsync before rename so the data is actually on disk, not
+    // merely in the OS page cache, before we commit.
+    if let Err(e) = tmp.write_all(bytes).and_then(|_| tmp.sync_data()) {
+        drop(tmp);
+        let _ = std::fs::remove_file(&tmp_path);
+        return Err(e);
+    }
+    drop(tmp);
+
+    // If the destination exists, carry over its permission bits to the
+    // temp file so the rename doesn't silently change mode. On Windows
+    // `set_permissions` only flips the read-only bit and ACLs are
+    // inherited from the parent directory, so this is effectively a no-op
+    // there; on Unix it preserves chmod state including +x.
+    if let Ok(dest_meta) = std::fs::metadata(path) {
+        let _ = std::fs::set_permissions(&tmp_path, dest_meta.permissions());
+    }
+
+    match std::fs::rename(&tmp_path, path) {
+        Ok(()) => Ok(()),
+        Err(e) => {
+            // Best-effort cleanup so we don't leak `.tmp` files when the
+            // rename itself fails (read-only target, cross-volume, etc.).
+            let _ = std::fs::remove_file(&tmp_path);
+            Err(e)
+        }
+    }
+}
+
+/// Generates unique temp paths even under SystemTime coarseness. Combines
+/// PID, a nanosecond timestamp, and a process-wide monotonically
+/// increasing counter so two callers that stat `SystemTime` inside the
+/// same tick still get distinct suffixes. Retries with a fresh counter
+/// value on `AlreadyExists` so a concurrent foreign file never wins the
+/// race.
+fn create_unique_temp(
+    parent: &Path,
+    file_name: &str,
+) -> std::io::Result<(std::path::PathBuf, std::fs::File)> {
+    static COUNTER: AtomicU64 = AtomicU64::new(0);
+    let pid = std::process::id();
+
+    // Bound the retries so a permanently unwriteable directory surfaces as
+    // an error instead of spinning forever.
+    for _ in 0..32 {
+        let nanos = std::time::SystemTime::now()
+            .duration_since(std::time::UNIX_EPOCH)
+            .map(|d| d.as_nanos())
+            .unwrap_or(0);
+        let seq = COUNTER.fetch_add(1, Ordering::Relaxed);
+        let tmp_path = parent.join(format!(".{}.{}.{}.{}.tmp", file_name, pid, nanos, seq));
+
+        match OpenOptions::new()
+            .write(true)
+            .create_new(true)
+            .open(&tmp_path)
+        {
+            Ok(file) => return Ok((tmp_path, file)),
+            Err(e) if e.kind() == std::io::ErrorKind::AlreadyExists => continue,
+            Err(e) => return Err(e),
+        }
+    }
+
+    Err(std::io::Error::other(
+        "could not allocate a unique temp file after 32 attempts",
+    ))
+}
+
+#[cfg(test)]
+mod tests {
+    use super::write_atomic;
+    use std::fs;
+    use std::sync::atomic::{AtomicU64, Ordering};
+
+    fn tmp_dir() -> std::path::PathBuf {
+        // Tests run in parallel by default. `SystemTime::now()` resolution
+        // on some platforms (notably older Windows) is 15.6 ms, which is
+        // coarse enough that two threads racing into this function share a
+        // nanos value. Add a process-wide atomic counter plus the current
+        // thread id so distinct test threads always get distinct paths.
+        static COUNTER: AtomicU64 = AtomicU64::new(0);
+        let seq = COUNTER.fetch_add(1, Ordering::Relaxed);
+        let tid = format!("{:?}", std::thread::current().id());
+        let tid_safe: String = tid
+            .chars()
+            .map(|c| if c.is_ascii_alphanumeric() { c } else { '_' })
+            .collect();
+        let base = std::env::temp_dir().join(format!(
+            "trixty-fs-atomic-{}-{}-{}-{}",
+            std::process::id(),
+            tid_safe,
+            std::time::SystemTime::now()
+                .duration_since(std::time::UNIX_EPOCH)
+                .map(|d| d.as_nanos())
+                .unwrap_or(0),
+            seq,
+        ));
+        fs::create_dir_all(&base).unwrap();
+        base
+    }
+
+    #[test]
+    fn writes_new_file() {
+        let dir = tmp_dir();
+        let target = dir.join("new.txt");
+        write_atomic(&target, b"hello").unwrap();
+        assert_eq!(fs::read_to_string(&target).unwrap(), "hello");
+        fs::remove_dir_all(&dir).ok();
+    }
+
+    #[test]
+    fn replaces_existing_file_contents() {
+        let dir = tmp_dir();
+        let target = dir.join("replace.txt");
+        fs::write(&target, b"old payload").unwrap();
+        write_atomic(&target, b"new payload").unwrap();
+        assert_eq!(fs::read_to_string(&target).unwrap(), "new payload");
+        fs::remove_dir_all(&dir).ok();
+    }
+
+    #[test]
+    fn leaves_no_temp_files_behind_after_success() {
+        let dir = tmp_dir();
+        let target = dir.join("clean.txt");
+        write_atomic(&target, b"payload").unwrap();
+        let leftovers: Vec<_> = fs::read_dir(&dir)
+            .unwrap()
+            .filter_map(|e| e.ok())
+            .filter(|e| e.file_name().to_string_lossy().ends_with(".tmp"))
+            .collect();
+        assert!(
+            leftovers.is_empty(),
+            "expected no .tmp leftovers, found: {:?}",
+            leftovers.iter().map(|e| e.file_name()).collect::<Vec<_>>()
+        );
+        fs::remove_dir_all(&dir).ok();
+    }
+
+    // Unix-only: the "executable bit lost on overwrite" regression the
+    // review flagged is only observable through the Unix permission
+    // model. On Windows `std::fs::Permissions` exposes only the
+    // read-only bit and ACLs are inherited from the parent directory,
+    // so there is no meaningful assertion beyond "the file still
+    // exists", which the other tests already cover.
+    #[cfg(unix)]
+    #[test]
+    fn preserves_unix_mode_bits_on_replace() {
+        use std::os::unix::fs::PermissionsExt;
+
+        let dir = tmp_dir();
+        let target = dir.join("perm.txt");
+        fs::write(&target, b"original").unwrap();
+
+        let mut perms = fs::metadata(&target).unwrap().permissions();
+        perms.set_mode(0o755);
+        fs::set_permissions(&target, perms).unwrap();
+
+        write_atomic(&target, b"replaced").unwrap();
+
+        let new_perms = fs::metadata(&target).unwrap().permissions();
+        assert_eq!(new_perms.mode() & 0o777, 0o755);
+
+        fs::remove_dir_all(&dir).ok();
+    }
+}
diff --git a/apps/desktop/src-tauri/src/lib.rs b/apps/desktop/src-tauri/src/lib.rs
index f84992fe..db7d7f57 100644
--- a/apps/desktop/src-tauri/src/lib.rs
+++ b/apps/desktop/src-tauri/src/lib.rs
@@ -1,5 +1,6 @@
 mod about;
 mod error;
+mod fs_atomic;
 mod http;
 mod pty;
 
@@ -200,7 +201,7 @@ fn read_file(path: String) -> Result<String, String> {
 
 #[tauri::command]
 fn write_file(path: String, content: String) -> Result<(), String> {
-    fs::write(&path, content).map_err(|e| {
+    fs_atomic::write_atomic(std::path::Path::new(&path), content.as_bytes()).map_err(|e| {
         let err = format!("Failed to write file {}: {}", path, e);
         error!("{}", err);
         redact_user_paths(&err)