diff --git a/src/app/features/room/thread/ThreadTimeline.tsx b/src/app/features/room/thread/ThreadTimeline.tsx
index e684f0a44..2f6f60e91 100644
--- a/src/app/features/room/thread/ThreadTimeline.tsx
+++ b/src/app/features/room/thread/ThreadTimeline.tsx
@@ -545,9 +545,19 @@ export function ThreadTimeline({ room, thread, editor }: ThreadTimelineProps) {
     [room, thread, setReplyDraft, editor],
   );
 
+  // Non-thread relations (reactions, edits) that target the thread root live only in
+  // the room's main timeline set (matrix-js-sdk Room.eventShouldLiveIn), so lookups
+  // for the root must use the room set instead of the thread set.
+  const getRelationTimelineSet = useCallback(
+    (eventId: string) =>
+      eventId === thread.id ? room.getUnfilteredTimelineSet() : thread.getUnfilteredTimelineSet(),
+    [room, thread],
+  );
+
   const handleReactionToggle = useCallback(
     (targetEventId: string, key: string, shortcode?: string) => {
-      const timelineSet = thread.getUnfilteredTimelineSet();
+      const isRoot = targetEventId === thread.id;
+      const timelineSet = getRelationTimelineSet(targetEventId);
       const relations = getEventReactions(timelineSet, targetEventId);
       const allReactions = relations?.getSortedAnnotationsByKey() ?? [];
       const [, reactionsSet] = allReactions.find(([k]) => k === key) ?? [];
@@ -563,13 +573,14 @@ export function ThreadTimeline({ room, thread, editor }: ThreadTimelineProps) {
         (reactions.find(eventWithShortcode)?.getContent().shortcode as string | undefined);
       mx.sendEvent(
         room.roomId,
-        thread.id,
+        // A reaction on the root is a main-timeline event, not a thread reply.
+        isRoot ? null : thread.id,
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         MessageEvent.Reaction as any,
         getReactionContent(targetEventId, key, rShortcode),
       );
     },
-    [mx, room, thread],
+    [mx, room, thread, getRelationTimelineSet],
   );
 
   const handleEdit = useCallback(
@@ -715,7 +726,7 @@ export function ThreadTimeline({ room, thread, editor }: ThreadTimelineProps) {
     ): ReactNode => {
       const mEventId = mEvent.getId();
       if (!mEventId) return null;
-      const timelineSet = thread.getUnfilteredTimelineSet();
+      const timelineSet = getRelationTimelineSet(mEventId);
       const reactionRelations = getEventReactions(timelineSet, mEventId);
       const reactions = reactionRelations?.getSortedAnnotationsByKey();
       const hasReactions = !!reactions && reactions.length > 0;
@@ -783,7 +794,6 @@ export function ThreadTimeline({ room, thread, editor }: ThreadTimelineProps) {
       );
     },
     [
-      thread,
       room,
       messageSpacing,
       messageLayout,
@@ -810,6 +820,7 @@ export function ThreadTimeline({ room, thread, editor }: ThreadTimelineProps) {
       lotusTerminal,
       mx,
       renderMessageContent,
+      getRelationTimelineSet,
     ],
   );