diff --git a/crates/matrix-sdk-crypto/CHANGELOG.md b/crates/matrix-sdk-crypto/CHANGELOG.md
index 14ff187ecd8..b5062c84fe8 100644
--- a/crates/matrix-sdk-crypto/CHANGELOG.md
+++ b/crates/matrix-sdk-crypto/CHANGELOG.md
@@ -8,6 +8,12 @@ Changed:
 
 Breaking changes:
 
+- Add a `backup_version` argument to `CryptoStore`'s
+  `inbound_group_sessions_for_backup`,
+  `mark_inbound_group_sessions_as_backed_up` and
+  `inbound_group_session_counts` methods.
+  ([#3253](https://github.com/matrix-org/matrix-rust-sdk/pull/3253))
+
 - Rename the `OlmMachine::invalidate_group_session` method to
   `OlmMachine::discard_room_key`
 
diff --git a/crates/matrix-sdk-crypto/src/backups/mod.rs b/crates/matrix-sdk-crypto/src/backups/mod.rs
index e89f867bf6a..4d6470f48d2 100644
--- a/crates/matrix-sdk-crypto/src/backups/mod.rs
+++ b/crates/matrix-sdk-crypto/src/backups/mod.rs
@@ -397,7 +397,8 @@ impl BackupMachine {
 
     /// Get the number of backed up room keys and the total number of room keys.
     pub async fn room_key_counts(&self) -> Result<RoomKeyCounts, CryptoStoreError> {
-        self.store.inbound_group_session_counts().await
+        let backup_version = self.backup_key.read().await.as_ref().and_then(|k| k.backup_version());
+        self.store.inbound_group_session_counts(backup_version.as_deref()).await
     }
 
     /// Disable and reset our backup state.
@@ -476,7 +477,12 @@ impl BackupMachine {
 
                 trace!(request_id = ?r.request_id, keys = ?r.sessions, "Marking room keys as backed up");
 
-                self.store.mark_inbound_group_sessions_as_backed_up(&room_and_session_ids).await?;
+                self.store
+                    .mark_inbound_group_sessions_as_backed_up(
+                        &r.request.version,
+                        &room_and_session_ids,
+                    )
+                    .await?;
 
                 trace!(
                     request_id = ?r.request_id,
@@ -514,7 +520,7 @@ impl BackupMachine {
         };
 
         let sessions =
-            self.store.inbound_group_sessions_for_backup(Self::BACKUP_BATCH_SIZE).await?;
+            self.store.inbound_group_sessions_for_backup(&version, Self::BACKUP_BATCH_SIZE).await?;
 
         if sessions.is_empty() {
             trace!(?backup_key, "No room keys need to be backed up");
@@ -619,6 +625,7 @@ mod tests {
     use ruma::{device_id, room_id, user_id, CanonicalJsonValue, DeviceId, RoomId, UserId};
     use serde_json::json;
 
+    use super::BackupMachine;
     use crate::{
         olm::BackedUpRoomKey, store::BackupDecryptionKey, types::RoomKeyBackupInfo, OlmError,
         OlmMachine,
@@ -658,7 +665,10 @@ mod tests {
 
     async fn backup_flow(machine: OlmMachine) -> Result<(), OlmError> {
         let backup_machine = machine.backup_machine();
-        let counts = backup_machine.store.inbound_group_session_counts().await?;
+        let backup_version = current_backup_version(backup_machine).await;
+
+        let counts =
+            backup_machine.store.inbound_group_session_counts(backup_version.as_deref()).await?;
 
         assert_eq!(counts.total, 0, "Initially no keys exist");
         assert_eq!(counts.backed_up, 0, "Initially no backed up keys exist");
@@ -666,7 +676,8 @@ mod tests {
         machine.create_outbound_group_session_with_defaults_test_helper(room_id()).await?;
         machine.create_outbound_group_session_with_defaults_test_helper(room_id2()).await?;
 
-        let counts = backup_machine.store.inbound_group_session_counts().await?;
+        let counts =
+            backup_machine.store.inbound_group_session_counts(backup_version.as_deref()).await?;
         assert_eq!(counts.total, 2, "Two room keys need to exist in the store");
         assert_eq!(counts.backed_up, 0, "No room keys have been backed up yet");
 
@@ -685,8 +696,10 @@ mod tests {
         );
 
         backup_machine.mark_request_as_sent(&request_id).await?;
+        let backup_version = current_backup_version(backup_machine).await;
 
-        let counts = backup_machine.store.inbound_group_session_counts().await?;
+        let counts =
+            backup_machine.store.inbound_group_session_counts(backup_version.as_deref()).await?;
         assert_eq!(counts.total, 2);
         assert_eq!(counts.backed_up, 2, "All room keys have been backed up");
 
@@ -696,8 +709,10 @@ mod tests {
         );
 
         backup_machine.disable_backup().await?;
+        let backup_version = current_backup_version(backup_machine).await;
 
-        let counts = backup_machine.store.inbound_group_session_counts().await?;
+        let counts =
+            backup_machine.store.inbound_group_session_counts(backup_version.as_deref()).await?;
         assert_eq!(counts.total, 2);
         assert_eq!(
             counts.backed_up, 0,
@@ -707,6 +722,10 @@ mod tests {
         Ok(())
     }
 
+    async fn current_backup_version(backup_machine: &BackupMachine) -> Option<String> {
+        backup_machine.backup_key.read().await.as_ref().and_then(|k| k.backup_version())
+    }
+
     #[async_test]
     async fn memory_store_backups() -> Result<(), OlmError> {
         let machine = OlmMachine::new(alice_id(), alice_device_id()).await;
diff --git a/crates/matrix-sdk-crypto/src/store/integration_tests.rs b/crates/matrix-sdk-crypto/src/store/integration_tests.rs
index f93828da879..025fc054d57 100644
--- a/crates/matrix-sdk-crypto/src/store/integration_tests.rs
+++ b/crates/matrix-sdk-crypto/src/store/integration_tests.rs
@@ -323,10 +323,10 @@ macro_rules! cryptostore_integration_tests {
                     .unwrap();
                 assert_eq!(session, loaded_session);
                 assert_eq!(store.get_inbound_group_sessions().await.unwrap().len(), 1);
-                assert_eq!(store.inbound_group_session_counts().await.unwrap().total, 1);
-                assert_eq!(store.inbound_group_session_counts().await.unwrap().backed_up, 0);
+                assert_eq!(store.inbound_group_session_counts(None).await.unwrap().total, 1);
+                assert_eq!(store.inbound_group_session_counts(None).await.unwrap().backed_up, 0);
 
-                let to_back_up = store.inbound_group_sessions_for_backup(1).await.unwrap();
+                let to_back_up = store.inbound_group_sessions_for_backup("bkpver", 1).await.unwrap();
                 assert_eq!(to_back_up, vec![session])
             }
 
@@ -342,14 +342,10 @@ macro_rules! cryptostore_integration_tests {
                 }
                 let changes = Changes { inbound_group_sessions: sessions.clone(), ..Default::default() };
                 store.save_changes(changes).await.expect("Can't save group session");
-                assert_eq!(store.inbound_group_sessions_for_backup(100).await.unwrap().len(), 10);
-
-                fn session_info(session: &InboundGroupSession) -> (&RoomId, &str) {
-                    (&session.room_id(), &session.session_id())
-                }
+                assert_eq!(store.inbound_group_sessions_for_backup("bkpver", 100).await.unwrap().len(), 10);
 
                 // When I mark some as backed up
-                store.mark_inbound_group_sessions_as_backed_up(&[
+                store.mark_inbound_group_sessions_as_backed_up("bkpver", &[
                     session_info(&sessions[1]),
                     session_info(&sessions[3]),
                     session_info(&sessions[5]),
@@ -358,7 +354,7 @@ macro_rules! cryptostore_integration_tests {
                 ]).await.expect("Failed to mark sessions as backed up");
 
                 // And ask which still need backing up
-                let to_back_up = store.inbound_group_sessions_for_backup(10).await.unwrap();
+                let to_back_up = store.inbound_group_sessions_for_backup("bkpver", 10).await.unwrap();
                 let needs_backing_up = |i: usize| to_back_up.iter().any(|s| s.session_id() == sessions[i].session_id());
 
                 // Then the sessions we said were backed up no longer need backing up
@@ -381,27 +377,35 @@ macro_rules! cryptostore_integration_tests {
             async fn reset_inbound_group_session_for_backup() {
                 let (account, store) =
                     get_loaded_store("reset_inbound_group_session_for_backup").await;
-                assert_eq!(store.inbound_group_session_counts().await.unwrap().total, 0);
+                assert_eq!(store.inbound_group_session_counts(None).await.unwrap().total, 0);
 
                 let room_id = &room_id!("!test:localhost");
                 let (_, session) = account.create_group_session_pair_with_defaults(room_id).await;
 
-                session.mark_as_backed_up();
-
                 let changes =
                     Changes { inbound_group_sessions: vec![session.clone()], ..Default::default() };
 
                 store.save_changes(changes).await.expect("Can't save group session");
 
-                assert_eq!(store.inbound_group_session_counts().await.unwrap().total, 1);
-                assert_eq!(store.inbound_group_session_counts().await.unwrap().backed_up, 1);
+                // Given we have backed up our session
+                store
+                    .mark_inbound_group_sessions_as_backed_up("bkpver1", &[session_info(&session)])
+                    .await
+                    .expect("Failed to mark_inbound_group_sessions_as_backed_up.");
+
+                assert_eq!(store.inbound_group_session_counts(Some("bkpver1")).await.unwrap().total, 1);
+                assert_eq!(store.inbound_group_session_counts(Some("bkpver1")).await.unwrap().backed_up, 1);
 
-                let to_back_up = store.inbound_group_sessions_for_backup(1).await.unwrap();
+                // Sanity: before resetting, we have nothing to back up
+                let to_back_up = store.inbound_group_sessions_for_backup("bkpver1", 1).await.unwrap();
                 assert_eq!(to_back_up, vec![]);
 
+                // When we reset the backup
                 store.reset_backup_state().await.unwrap();
 
-                let to_back_up = store.inbound_group_sessions_for_backup(1).await.unwrap();
+                // Then after resetting, even if we supply the same backup version number, we need
+                // to back up the session
+                let to_back_up = store.inbound_group_sessions_for_backup("bkpver1", 1).await.unwrap();
                 assert_eq!(to_back_up, vec![session]);
             }
 
@@ -438,7 +442,7 @@ macro_rules! cryptostore_integration_tests {
                 loaded_session.export().await;
 
                 assert_eq!(store.get_inbound_group_sessions().await.unwrap().len(), 1);
-                assert_eq!(store.inbound_group_session_counts().await.unwrap().total, 1);
+                assert_eq!(store.inbound_group_session_counts(None).await.unwrap().total, 1);
             }
 
             #[async_test]
@@ -960,6 +964,10 @@ macro_rules! cryptostore_integration_tests {
                 let loaded_2 = store.get_custom_value("B").await.unwrap();
                 assert_eq!(None, loaded_2);
             }
+
+            fn session_info(session: &InboundGroupSession) -> (&RoomId, &str) {
+                (&session.room_id(), &session.session_id())
+            }
         }
     };
 }
diff --git a/crates/matrix-sdk-crypto/src/store/memorystore.rs b/crates/matrix-sdk-crypto/src/store/memorystore.rs
index 54339756c7f..b500285f28c 100644
--- a/crates/matrix-sdk-crypto/src/store/memorystore.rs
+++ b/crates/matrix-sdk-crypto/src/store/memorystore.rs
@@ -270,7 +270,10 @@ impl CryptoStore for MemoryStore {
         Ok(self.inbound_group_sessions.get_all())
     }
 
-    async fn inbound_group_session_counts(&self) -> Result<RoomKeyCounts> {
+    async fn inbound_group_session_counts(
+        &self,
+        _backup_version: Option<&str>,
+    ) -> Result<RoomKeyCounts> {
         let backed_up =
             self.get_inbound_group_sessions().await?.into_iter().filter(|s| s.backed_up()).count();
 
@@ -279,6 +282,7 @@ impl CryptoStore for MemoryStore {
 
     async fn inbound_group_sessions_for_backup(
         &self,
+        _backup_version: &str,
         limit: usize,
     ) -> Result<Vec<InboundGroupSession>> {
         Ok(self
@@ -292,6 +296,7 @@ impl CryptoStore for MemoryStore {
 
     async fn mark_inbound_group_sessions_as_backed_up(
         &self,
+        _backup_version: &str,
         room_and_session_ids: &[(&RoomId, &str)],
     ) -> Result<()> {
         for (room_id, session_id) in room_and_session_ids {
@@ -758,22 +763,29 @@ mod integration_tests {
             self.0.get_inbound_group_sessions().await
         }
 
-        async fn inbound_group_session_counts(&self) -> Result<RoomKeyCounts, Self::Error> {
-            self.0.inbound_group_session_counts().await
+        async fn inbound_group_session_counts(
+            &self,
+            backup_version: Option<&str>,
+        ) -> Result<RoomKeyCounts, Self::Error> {
+            self.0.inbound_group_session_counts(backup_version).await
         }
 
         async fn inbound_group_sessions_for_backup(
             &self,
+            backup_version: &str,
             limit: usize,
         ) -> Result<Vec<InboundGroupSession>, Self::Error> {
-            self.0.inbound_group_sessions_for_backup(limit).await
+            self.0.inbound_group_sessions_for_backup(backup_version, limit).await
         }
 
         async fn mark_inbound_group_sessions_as_backed_up(
             &self,
+            backup_version: &str,
             room_and_session_ids: &[(&RoomId, &str)],
         ) -> Result<(), Self::Error> {
-            self.0.mark_inbound_group_sessions_as_backed_up(room_and_session_ids).await
+            self.0
+                .mark_inbound_group_sessions_as_backed_up(backup_version, room_and_session_ids)
+                .await
         }
 
         async fn reset_backup_state(&self) -> Result<(), Self::Error> {
diff --git a/crates/matrix-sdk-crypto/src/store/traits.rs b/crates/matrix-sdk-crypto/src/store/traits.rs
index 3347f373d77..f8fe5f19488 100644
--- a/crates/matrix-sdk-crypto/src/store/traits.rs
+++ b/crates/matrix-sdk-crypto/src/store/traits.rs
@@ -105,22 +105,43 @@ pub trait CryptoStore: AsyncTraitDeps {
 
     /// Get the number inbound group sessions we have and how many of them are
     /// backed up.
-    async fn inbound_group_session_counts(&self) -> Result<RoomKeyCounts, Self::Error>;
+    async fn inbound_group_session_counts(
+        &self,
+        backup_version: Option<&str>,
+    ) -> Result<RoomKeyCounts, Self::Error>;
 
-    /// Get all the inbound group sessions we have not backed up yet.
+    /// Return a batch of ['InboundGroupSession'] ("room keys") that have not
+    /// yet been backed up in the supplied backup version.
+    ///
+    /// The size of the returned `Vec` is <= `limit`.
+    ///
+    /// Note: some implementations ignore `backup_version` and assume the
+    /// current backup version, which is normally the same.
     async fn inbound_group_sessions_for_backup(
         &self,
+        backup_version: &str,
         limit: usize,
     ) -> Result<Vec<InboundGroupSession>, Self::Error>;
 
-    /// Mark the inbound group sessions with the supplied room and session IDs
-    /// as backed up
+    /// Store the fact that the supplied sessions were backed up into the backup
+    /// with version `backup_version`.
+    ///
+    /// Note: some implementations ignore `backup_version` and assume the
+    /// current backup version, which is normally the same.
     async fn mark_inbound_group_sessions_as_backed_up(
         &self,
+        backup_version: &str,
         room_and_session_ids: &[(&RoomId, &str)],
     ) -> Result<(), Self::Error>;
 
     /// Reset the backup state of all the stored inbound group sessions.
+    ///
+    /// Note: this is mostly implemented by stores that ignore the
+    /// `backup_version` argument on `inbound_group_sessions_for_backup` and
+    /// `mark_inbound_group_sessions_as_backed_up`. Implementations that
+    /// pay attention to the supplied backup version probably don't need to
+    /// update their storage when the current backup version changes, so have
+    /// empty implementations of this method.
     async fn reset_backup_state(&self) -> Result<(), Self::Error>;
 
     /// Get the backup keys we have stored.
@@ -331,23 +352,27 @@ impl<T: CryptoStore> CryptoStore for EraseCryptoStoreError<T> {
         self.0.get_inbound_group_sessions().await.map_err(Into::into)
     }
 
-    async fn inbound_group_session_counts(&self) -> Result<RoomKeyCounts> {
-        self.0.inbound_group_session_counts().await.map_err(Into::into)
+    async fn inbound_group_session_counts(
+        &self,
+        backup_version: Option<&str>,
+    ) -> Result<RoomKeyCounts> {
+        self.0.inbound_group_session_counts(backup_version).await.map_err(Into::into)
     }
-
     async fn inbound_group_sessions_for_backup(
         &self,
+        backup_version: &str,
         limit: usize,
     ) -> Result<Vec<InboundGroupSession>> {
-        self.0.inbound_group_sessions_for_backup(limit).await.map_err(Into::into)
+        self.0.inbound_group_sessions_for_backup(backup_version, limit).await.map_err(Into::into)
     }
 
     async fn mark_inbound_group_sessions_as_backed_up(
         &self,
+        backup_version: &str,
         room_and_session_ids: &[(&RoomId, &str)],
     ) -> Result<()> {
         self.0
-            .mark_inbound_group_sessions_as_backed_up(room_and_session_ids)
+            .mark_inbound_group_sessions_as_backed_up(backup_version, room_and_session_ids)
             .await
             .map_err(Into::into)
     }
diff --git a/crates/matrix-sdk-indexeddb/src/crypto_store/mod.rs b/crates/matrix-sdk-indexeddb/src/crypto_store/mod.rs
index 2b594c42cf0..3faf6f64390 100644
--- a/crates/matrix-sdk-indexeddb/src/crypto_store/mod.rs
+++ b/crates/matrix-sdk-indexeddb/src/crypto_store/mod.rs
@@ -873,7 +873,7 @@ impl_crypto_store! {
         ).await
     }
 
-    async fn inbound_group_session_counts(&self) -> Result<RoomKeyCounts> {
+    async fn inbound_group_session_counts(&self, _backup_version: Option<&str>) -> Result<RoomKeyCounts> {
         let tx = self
             .inner
             .transaction_on_one_with_mode(
@@ -889,6 +889,7 @@ impl_crypto_store! {
 
     async fn inbound_group_sessions_for_backup(
         &self,
+        _backup_version: &str,
         limit: usize,
     ) -> Result<Vec<InboundGroupSession>> {
         let tx = self
@@ -933,7 +934,10 @@ impl_crypto_store! {
         Ok(result)
     }
 
-    async fn mark_inbound_group_sessions_as_backed_up(&self, room_and_session_ids: &[(&RoomId, &str)]) -> Result<()> {
+    async fn mark_inbound_group_sessions_as_backed_up(&self,
+        _backup_version: &str,
+        room_and_session_ids: &[(&RoomId, &str)]
+    ) -> Result<()> {
         let tx = self
             .inner
             .transaction_on_one_with_mode(
diff --git a/crates/matrix-sdk-sqlite/src/crypto_store.rs b/crates/matrix-sdk-sqlite/src/crypto_store.rs
index 522f2acbb00..61216566201 100644
--- a/crates/matrix-sdk-sqlite/src/crypto_store.rs
+++ b/crates/matrix-sdk-sqlite/src/crypto_store.rs
@@ -477,7 +477,10 @@ trait SqliteObjectCryptoStoreExt: SqliteObjectExt {
             .await?)
     }
 
-    async fn get_inbound_group_session_counts(&self) -> Result<RoomKeyCounts> {
+    async fn get_inbound_group_session_counts(
+        &self,
+        _backup_version: Option<&str>,
+    ) -> Result<RoomKeyCounts> {
         let total = self
             .query_row("SELECT count(*) FROM inbound_group_session", (), |row| row.get(0))
             .await?;
@@ -940,12 +943,16 @@ impl CryptoStore for SqliteCryptoStore {
             .collect()
     }
 
-    async fn inbound_group_session_counts(&self) -> Result<RoomKeyCounts> {
-        Ok(self.acquire().await?.get_inbound_group_session_counts().await?)
+    async fn inbound_group_session_counts(
+        &self,
+        backup_version: Option<&str>,
+    ) -> Result<RoomKeyCounts> {
+        Ok(self.acquire().await?.get_inbound_group_session_counts(backup_version).await?)
     }
 
     async fn inbound_group_sessions_for_backup(
         &self,
+        _backup_version: &str,
         limit: usize,
     ) -> Result<Vec<InboundGroupSession>> {
         self.acquire()
@@ -962,6 +969,7 @@ impl CryptoStore for SqliteCryptoStore {
 
     async fn mark_inbound_group_sessions_as_backed_up(
         &self,
+        _backup_version: &str,
         session_ids: &[(&RoomId, &str)],
     ) -> Result<()> {
         Ok(self