diff --git a/crates/matrix-sdk-crypto/src/store/memorystore.rs b/crates/matrix-sdk-crypto/src/store/memorystore.rs
index a45d6e99e..54339756c 100644
--- a/crates/matrix-sdk-crypto/src/store/memorystore.rs
+++ b/crates/matrix-sdk-crypto/src/store/memorystore.rs
@@ -56,7 +56,7 @@ pub struct MemoryStore {
     inbound_group_sessions: GroupSessionStore,
     outbound_group_sessions: StdRwLock<BTreeMap<OwnedRoomId, OutboundGroupSession>>,
     private_identity: StdRwLock<Option<PrivateCrossSigningIdentity>>,
-    tracked_users: StdRwLock<Vec<TrackedUser>>,
+    tracked_users: StdRwLock<HashMap<OwnedUserId, TrackedUser>>,
     olm_hashes: StdRwLock<HashMap<String, HashSet<String>>>,
     devices: DeviceStore,
     identities: StdRwLock<HashMap<OwnedUserId, ReadOnlyUserIdentities>>,
@@ -324,12 +324,13 @@ impl CryptoStore for MemoryStore {
     }
 
     async fn load_tracked_users(&self) -> Result<Vec<TrackedUser>> {
-        Ok(self.tracked_users.read().unwrap().clone())
+        Ok(self.tracked_users.read().unwrap().values().cloned().collect())
     }
 
     async fn save_tracked_users(&self, tracked_users: &[(&UserId, bool)]) -> Result<()> {
         self.tracked_users.write().unwrap().extend(tracked_users.iter().map(|(user_id, dirty)| {
-            TrackedUser { user_id: user_id.to_owned().into(), dirty: *dirty }
+            let user_id: OwnedUserId = user_id.to_owned().into();
+            (user_id.clone(), TrackedUser { user_id, dirty: *dirty })
         }));
         Ok(())
     }
@@ -559,23 +560,29 @@ mod tests {
     }
 
     #[async_test]
-    async fn test_tracked_users_store() {
-        // Given some tracked users
-        let tracked_users =
-            &[(user_id!("@dirty_user:s"), true), (user_id!("@clean_user:t"), false)];
-
-        // When we save them to the store
+    async fn test_tracked_users_are_stored_once_per_user_id() {
+        // Given a store containing 2 tracked users, both dirty
+        let user1 = user_id!("@user1:s");
+        let user2 = user_id!("@user2:s");
+        let user3 = user_id!("@user3:s");
         let store = MemoryStore::new();
-        store.save_tracked_users(tracked_users).await.unwrap();
+        store.save_tracked_users(&[(user1, true), (user2, true)]).await.unwrap();
 
-        // Then we can get them out again
+        // When we mark one as clean and add another
+        store.save_tracked_users(&[(user2, false), (user3, false)]).await.unwrap();
+
+        // Then we can get them out again and their dirty flags are correct
         let loaded_tracked_users =
             store.load_tracked_users().await.expect("failed to load tracked users");
-        assert_eq!(loaded_tracked_users[0].user_id, user_id!("@dirty_user:s"));
-        assert!(loaded_tracked_users[0].dirty);
-        assert_eq!(loaded_tracked_users[1].user_id, user_id!("@clean_user:t"));
-        assert!(!loaded_tracked_users[1].dirty);
-        assert_eq!(loaded_tracked_users.len(), 2);
+
+        let tracked_contains = |user_id, dirty| {
+            loaded_tracked_users.iter().any(|u| u.user_id == user_id && u.dirty == dirty)
+        };
+
+        assert!(tracked_contains(user1, true));
+        assert!(tracked_contains(user2, false));
+        assert!(tracked_contains(user3, false));
+        assert_eq!(loaded_tracked_users.len(), 3);
     }
 
     #[async_test]
diff --git a/crates/matrix-sdk-crypto/src/store/traits.rs b/crates/matrix-sdk-crypto/src/store/traits.rs
index bebcdd03b..3347f373d 100644
--- a/crates/matrix-sdk-crypto/src/store/traits.rs
+++ b/crates/matrix-sdk-crypto/src/store/traits.rs
@@ -133,11 +133,14 @@ pub trait CryptoStore: AsyncTraitDeps {
         room_id: &RoomId,
     ) -> Result<Option<OutboundGroupSession>, Self::Error>;
 
-    /// Load the list of users whose devices we are keeping track of.
+    /// Provide the list of users whose devices we are keeping track of, and
+    /// whether they are considered dirty/outdated.
     async fn load_tracked_users(&self) -> Result<Vec<TrackedUser>, Self::Error>;
 
-    /// Save a list of users and their respective dirty/outdated flags to the
-    /// store.
+    /// Update the list of users whose devices we are keeping track of, and
+    /// whether they are considered dirty/outdated.
+    ///
+    /// Replaces any existing entry with a matching user ID.
     async fn save_tracked_users(&self, users: &[(&UserId, bool)]) -> Result<(), Self::Error>;
 
     /// Get the device for the given user with the given device ID.