diff --git a/apps/wakunode2/wakunode2.nim b/apps/wakunode2/wakunode2.nim
index ad15452ee..263bfac70 100644
--- a/apps/wakunode2/wakunode2.nim
+++ b/apps/wakunode2/wakunode2.nim
@@ -28,12 +28,12 @@ import
   ../../waku/v2/node/peer_manager/peer_store/migrations as peer_store_sqlite_migrations,
   ../../waku/v2/node/dnsdisc/waku_dnsdisc,
   ../../waku/v2/node/discv5/waku_discv5,
-  ../../waku/v2/node/storage/migration,
-  ../../waku/v2/node/storage/message/waku_store_queue,
-  ../../waku/v2/node/storage/message/sqlite_store,
-  ../../waku/v2/node/storage/message/message_retention_policy,
-  ../../waku/v2/node/storage/message/message_retention_policy_capacity,
-  ../../waku/v2/node/storage/message/message_retention_policy_time,
+  ../../waku/v2/node/message_store/sqlite_store/migrations as message_store_sqlite_migrations,
+  ../../waku/v2/node/message_store/waku_store_queue,
+  ../../waku/v2/node/message_store/sqlite_store,
+  ../../waku/v2/node/message_store/message_retention_policy,
+  ../../waku/v2/node/message_store/message_retention_policy_capacity,
+  ../../waku/v2/node/message_store/message_retention_policy_time,
   ../../waku/v2/node/wakuswitch, 
   ../../waku/v2/node/waku_node,
   ../../waku/v2/node/waku_metrics,
@@ -104,15 +104,6 @@ proc performSqliteVacuum(db: SqliteDatabase): SetupResult[void] =
 
   debug "finished sqlite database vacuuming"
 
-proc performDbMigration(db: SqliteDatabase, migrationPath: string): SetupResult[void] =
-  ## Run migration scripts on persistent storage
-  debug "starting sqlite database migration"
-  let migrationRes = db.migrate(migrationPath)
-  if migrationRes.isErr():
-    return err("failed to execute migration scripts: " & migrationRes.error)
-
-  debug "finished sqlite database migration"
-
 
 const PeerPersistenceDbUrl = "sqlite://peers.db"
 
@@ -189,7 +180,7 @@ proc setupMessageStorage(dbUrl: string, vacuum: bool, migrate: bool): SetupResul
 
   # Database migration
     if migrate:
-      ?performDbMigration(db.get(), migrationPath=MessageStoreMigrationPath)
+      ?message_store_sqlite_migrations.migrate(db.get())
 
   # TODO: Extract capacity from `messageRetentionPolicy`
   return setupMessagesStore(db, storeCapacity=high(int))
diff --git a/tests/v2/test_jsonrpc_waku.nim b/tests/v2/test_jsonrpc_waku.nim
index 8395fa50c..4f40cf5e9 100644
--- a/tests/v2/test_jsonrpc_waku.nim
+++ b/tests/v2/test_jsonrpc_waku.nim
@@ -14,7 +14,7 @@ import
   libp2p/protocols/pubsub/rpc/message
 import
   ../../waku/v1/node/rpc/hexstrings,
-  ../../waku/v2/node/storage/message/waku_store_queue,
+  ../../waku/v2/node/message_store/waku_store_queue,
   ../../waku/v2/node/waku_node,
   ../../waku/v2/node/jsonrpc/[store_api,
                               relay_api,
diff --git a/tests/v2/test_message_store_queue.nim b/tests/v2/test_message_store_queue.nim
index 045f32c7d..64c43127f 100644
--- a/tests/v2/test_message_store_queue.nim
+++ b/tests/v2/test_message_store_queue.nim
@@ -5,7 +5,7 @@ import
   stew/results,
   testutils/unittests
 import
-  ../../waku/v2/node/storage/message/waku_store_queue,
+  ../../waku/v2/node/message_store/waku_store_queue,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store,
   ../../waku/v2/utils/time
diff --git a/tests/v2/test_message_store_queue_index.nim b/tests/v2/test_message_store_queue_index.nim
index 3d2142efa..9af768983 100644
--- a/tests/v2/test_message_store_queue_index.nim
+++ b/tests/v2/test_message_store_queue_index.nim
@@ -8,7 +8,7 @@ import
 import
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/utils/time,
-  ../../waku/v2/node/storage/message/queue_store/index,
+  ../../waku/v2/node/message_store/queue_store/index,
   ./testlib/common
 
 
diff --git a/tests/v2/test_message_store_queue_pagination.nim b/tests/v2/test_message_store_queue_pagination.nim
index 73fe105b8..af932b42b 100644
--- a/tests/v2/test_message_store_queue_pagination.nim
+++ b/tests/v2/test_message_store_queue_pagination.nim
@@ -6,7 +6,7 @@ import
   nimcrypto/sha2,
   libp2p/protobuf/minprotobuf
 import
-  ../../waku/v2/node/storage/message/waku_store_queue,
+  ../../waku/v2/node/message_store/waku_store_queue,
   ../../waku/v2/protocol/waku_store,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/utils/time,
diff --git a/tests/v2/test_message_store_sqlite.nim b/tests/v2/test_message_store_sqlite.nim
index 541325d3b..a5df6ea5a 100644
--- a/tests/v2/test_message_store_sqlite.nim
+++ b/tests/v2/test_message_store_sqlite.nim
@@ -6,9 +6,9 @@ import
   chronos
 import
   ../../waku/common/sqlite,
-  ../../waku/v2/node/storage/message/sqlite_store,
-  ../../waku/v2/node/storage/message/message_retention_policy,
-  ../../waku/v2/node/storage/message/message_retention_policy_capacity,
+  ../../waku/v2/node/message_store/sqlite_store,
+  ../../waku/v2/node/message_store/message_retention_policy,
+  ../../waku/v2/node/message_store/message_retention_policy_capacity,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store/pagination,
   ../../waku/v2/utils/time,
diff --git a/tests/v2/test_message_store_sqlite_query.nim b/tests/v2/test_message_store_sqlite_query.nim
index c4e5ac52c..54fff2aec 100644
--- a/tests/v2/test_message_store_sqlite_query.nim
+++ b/tests/v2/test_message_store_sqlite_query.nim
@@ -6,7 +6,7 @@ import
   chronos
 import
   ../../waku/common/sqlite,
-  ../../waku/v2/node/storage/message/sqlite_store,
+  ../../waku/v2/node/message_store/sqlite_store,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store/pagination,
   ./utils,
diff --git a/tests/v2/test_waku_store.nim b/tests/v2/test_waku_store.nim
index 5a3e83530..bb4d1a575 100644
--- a/tests/v2/test_waku_store.nim
+++ b/tests/v2/test_waku_store.nim
@@ -7,8 +7,8 @@ import
   libp2p/crypto/crypto
 import
   ../../waku/common/sqlite,
-  ../../waku/v2/node/storage/message/waku_store_queue,
-  ../../waku/v2/node/storage/message/sqlite_store,
+  ../../waku/v2/node/message_store/waku_store_queue,
+  ../../waku/v2/node/message_store/sqlite_store,
   ../../waku/v2/node/peer_manager/peer_manager,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store,
diff --git a/tests/v2/test_waku_store_client.nim b/tests/v2/test_waku_store_client.nim
index aa04f986f..77e0611ed 100644
--- a/tests/v2/test_waku_store_client.nim
+++ b/tests/v2/test_waku_store_client.nim
@@ -7,7 +7,7 @@ import
   libp2p/crypto/crypto
 import
   ../../waku/common/sqlite,
-  ../../waku/v2/node/storage/message/sqlite_store,
+  ../../waku/v2/node/message_store/sqlite_store,
   ../../waku/v2/node/peer_manager/peer_manager,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store,
diff --git a/tests/v2/test_waku_store_resume.nim b/tests/v2/test_waku_store_resume.nim
index 1bb9e2c65..a00c30577 100644
--- a/tests/v2/test_waku_store_resume.nim
+++ b/tests/v2/test_waku_store_resume.nim
@@ -8,7 +8,7 @@ import
   libp2p/crypto/crypto
 import
   ../../waku/common/sqlite,
-  ../../waku/v2/node/storage/message/sqlite_store,
+  ../../waku/v2/node/message_store/sqlite_store,
   ../../waku/v2/node/peer_manager/peer_manager,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store,
diff --git a/tests/v2/test_waku_swap.nim b/tests/v2/test_waku_swap.nim
index 79e24b99d..96e1a26db 100644
--- a/tests/v2/test_waku_swap.nim
+++ b/tests/v2/test_waku_swap.nim
@@ -15,7 +15,7 @@ import
 import
   ../../waku/v2/protocol/waku_store,
   ../../waku/v2/protocol/waku_swap/waku_swap,
-  ../../waku/v2/node/storage/message/waku_store_queue,
+  ../../waku/v2/node/message_store/waku_store_queue,
   ../../waku/v2/node/waku_node,
   ../../waku/v2/utils/peers,
   ../test_helpers, 
diff --git a/tests/v2/test_wakunode_store.nim b/tests/v2/test_wakunode_store.nim
index 267219def..783544c91 100644
--- a/tests/v2/test_wakunode_store.nim
+++ b/tests/v2/test_wakunode_store.nim
@@ -14,8 +14,8 @@ import
   libp2p/protocols/pubsub/gossipsub
 import
   ../../waku/common/sqlite,
-  ../../waku/v2/node/storage/message/sqlite_store,
-  ../../waku/v2/node/storage/message/waku_store_queue,
+  ../../waku/v2/node/message_store/sqlite_store,
+  ../../waku/v2/node/message_store/waku_store_queue,
   ../../waku/v2/protocol/waku_message,
   ../../waku/v2/protocol/waku_store,
   ../../waku/v2/protocol/waku_filter,
diff --git a/waku/v2/node/storage/message/message_retention_policy.nim b/waku/v2/node/message_store/message_retention_policy.nim
similarity index 88%
rename from waku/v2/node/storage/message/message_retention_policy.nim
rename to waku/v2/node/message_store/message_retention_policy.nim
index 2a3a9fa78..fa0eafe03 100644
--- a/waku/v2/node/storage/message/message_retention_policy.nim
+++ b/waku/v2/node/message_store/message_retention_policy.nim
@@ -6,7 +6,7 @@ else:
 import
   stew/results
 import
-  ../../../protocol/waku_store/message_store
+  ../../protocol/waku_store/message_store
 
 type RetentionPolicyResult*[T] = Result[T, string]
 
diff --git a/waku/v2/node/storage/message/message_retention_policy_capacity.nim b/waku/v2/node/message_store/message_retention_policy_capacity.nim
similarity index 98%
rename from waku/v2/node/storage/message/message_retention_policy_capacity.nim
rename to waku/v2/node/message_store/message_retention_policy_capacity.nim
index d682a5b1c..f92a442d6 100644
--- a/waku/v2/node/storage/message/message_retention_policy_capacity.nim
+++ b/waku/v2/node/message_store/message_retention_policy_capacity.nim
@@ -7,7 +7,7 @@ import
   stew/results,
   chronicles
 import
-  ../../../protocol/waku_store/message_store,
+  ../../protocol/waku_store/message_store,
   ./message_retention_policy
 
 logScope:
diff --git a/waku/v2/node/storage/message/message_retention_policy_time.nim b/waku/v2/node/message_store/message_retention_policy_time.nim
similarity index 95%
rename from waku/v2/node/storage/message/message_retention_policy_time.nim
rename to waku/v2/node/message_store/message_retention_policy_time.nim
index f5504f1e8..443bffdc8 100644
--- a/waku/v2/node/storage/message/message_retention_policy_time.nim
+++ b/waku/v2/node/message_store/message_retention_policy_time.nim
@@ -9,8 +9,8 @@ import
   chronicles,
   chronos
 import
-  ../../../protocol/waku_store/message_store,
-  ../../../utils/time,
+  ../../protocol/waku_store/message_store,
+  ../../utils/time,
   ./message_retention_policy
 
 logScope:
diff --git a/waku/v2/node/storage/message/queue_store/index.nim b/waku/v2/node/message_store/queue_store/index.nim
similarity index 95%
rename from waku/v2/node/storage/message/queue_store/index.nim
rename to waku/v2/node/message_store/queue_store/index.nim
index ff02c2794..e1260bc24 100644
--- a/waku/v2/node/storage/message/queue_store/index.nim
+++ b/waku/v2/node/message_store/queue_store/index.nim
@@ -7,9 +7,9 @@ import
   stew/byteutils,
   nimcrypto/sha2
 import
-  ../../../../protocol/waku_message,
-  ../../../../protocol/waku_store/pagination,
-  ../../../../utils/time
+  ../../../protocol/waku_message,
+  ../../../protocol/waku_store/pagination,
+  ../../../utils/time
 
 
 type Index* = object
diff --git a/waku/v2/node/storage/message/queue_store/queue_store.nim b/waku/v2/node/message_store/queue_store/queue_store.nim
similarity index 98%
rename from waku/v2/node/storage/message/queue_store/queue_store.nim
rename to waku/v2/node/message_store/queue_store/queue_store.nim
index 6feb21f41..49482d37a 100644
--- a/waku/v2/node/storage/message/queue_store/queue_store.nim
+++ b/waku/v2/node/message_store/queue_store/queue_store.nim
@@ -8,11 +8,11 @@ import
   stew/[results, sorted_set],
   chronicles
 import
-  ../../../../protocol/waku_message,
-  ../../../../protocol/waku_store/rpc,
-  ../../../../protocol/waku_store/pagination,
-  ../../../../protocol/waku_store/message_store,
-  ../../../../utils/time,
+  ../../../protocol/waku_message,
+  ../../../protocol/waku_store/rpc,
+  ../../../protocol/waku_store/pagination,
+  ../../../protocol/waku_store/message_store,
+  ../../../utils/time,
   ./index
 
 
diff --git a/waku/v2/node/storage/message/sqlite_store.nim b/waku/v2/node/message_store/sqlite_store.nim
similarity index 100%
rename from waku/v2/node/storage/message/sqlite_store.nim
rename to waku/v2/node/message_store/sqlite_store.nim
diff --git a/waku/v2/node/message_store/sqlite_store/migrations.nim b/waku/v2/node/message_store/sqlite_store/migrations.nim
new file mode 100644
index 000000000..e0c764883
--- /dev/null
+++ b/waku/v2/node/message_store/sqlite_store/migrations.nim
@@ -0,0 +1,38 @@
+{.push raises: [].}
+
+import
+  std/[tables, strutils, os],
+  stew/results,
+  chronicles
+import
+  ../../../../common/sqlite,
+  ../../../../common/sqlite/migrations
+
+
+logScope:
+  topics = "message_store.migration"
+
+
+const SchemaVersion* = 7 # increase this when there is an update in the database schema
+
+template projectRoot: string = currentSourcePath.rsplit(DirSep, 1)[0] / ".." / ".." / ".." / ".." / ".."
+const MessageStoreMigrationPath: string = projectRoot / "migrations" / "message_store"
+
+
+proc migrate*(db: SqliteDatabase, targetVersion = SchemaVersion): DatabaseResult[void] = 
+  ## Compares the `user_version` of the sqlite database with the provided `targetVersion`, then
+  ## it runs migration scripts if the `user_version` is outdated. The `migrationScriptsDir` path
+  ## points to the directory holding the migrations scripts once the db is updated, it sets the
+  ## `user_version` to the `tragetVersion`.
+  ## 
+  ## If not `targetVersion` is provided, it defaults to `SchemaVersion`.
+  ##
+  ## NOTE: Down migration it is not currently supported
+  debug "starting message store's sqlite database migration"
+
+  let migrationRes = migrations.migrate(db, targetVersion, migrationsScriptsDir=MessageStoreMigrationPath)
+  if migrationRes.isErr():
+    return err("failed to execute migration scripts: " & migrationRes.error)
+
+  debug "finished message store's sqlite database migration"
+  ok()
diff --git a/waku/v2/node/storage/message/sqlite_store/queries.nim b/waku/v2/node/message_store/sqlite_store/queries.nim
similarity index 99%
rename from waku/v2/node/storage/message/sqlite_store/queries.nim
rename to waku/v2/node/message_store/sqlite_store/queries.nim
index e33c5af0f..8e55f0626 100644
--- a/waku/v2/node/storage/message/sqlite_store/queries.nim
+++ b/waku/v2/node/message_store/sqlite_store/queries.nim
@@ -8,9 +8,9 @@ import
   stew/[results, byteutils],
   sqlite3_abi
 import
-  ../../../../../common/sqlite, 
-  ../../../../protocol/waku_message,
-  ../../../../utils/time
+  ../../../../common/sqlite, 
+  ../../../protocol/waku_message,
+  ../../../utils/time
 
 
 const DbTable = "Message"
diff --git a/waku/v2/node/storage/message/sqlite_store/sqlite_store.nim b/waku/v2/node/message_store/sqlite_store/sqlite_store.nim
similarity index 95%
rename from waku/v2/node/storage/message/sqlite_store/sqlite_store.nim
rename to waku/v2/node/message_store/sqlite_store/sqlite_store.nim
index b11305a59..72d6f16bc 100644
--- a/waku/v2/node/storage/message/sqlite_store/sqlite_store.nim
+++ b/waku/v2/node/message_store/sqlite_store/sqlite_store.nim
@@ -10,11 +10,11 @@ import
   stew/[byteutils, results],
   chronicles
 import
-  ../../../../../common/sqlite,
-  ../../../../protocol/waku_message,
-  ../../../../protocol/waku_store/pagination,
-  ../../../../protocol/waku_store/message_store,
-  ../../../../utils/time,
+  ../../../../common/sqlite,
+  ../../../protocol/waku_message,
+  ../../../protocol/waku_store/pagination,
+  ../../../protocol/waku_store/message_store,
+  ../../../utils/time,
   ./queries
 
 logScope:
diff --git a/waku/v2/node/storage/message/waku_store_queue.nim b/waku/v2/node/message_store/waku_store_queue.nim
similarity index 100%
rename from waku/v2/node/storage/message/waku_store_queue.nim
rename to waku/v2/node/message_store/waku_store_queue.nim
diff --git a/waku/v2/node/storage/message/dual_message_store.nim b/waku/v2/node/storage/message/dual_message_store.nim
deleted file mode 100644
index 54edec79f..000000000
--- a/waku/v2/node/storage/message/dual_message_store.nim
+++ /dev/null
@@ -1,91 +0,0 @@
-{.push raises: [Defect].}
-
-import
-  std/options,
-  stew/results,
-  chronicles
-import
-  ../../../protocol/waku_message,
-  ../../../protocol/waku_store/pagination,
-  ../../../protocol/waku_store/message_store,
-  ../../../utils/time,
-  ../sqlite,
-  ./waku_store_queue,
-  ./sqlite_store
-
-logScope:
-  topics = "message_store.dual"
-
-
-type DualMessageStore* = ref object of MessageStore
-    inmemory: StoreQueueRef
-    persistent: SqliteStore
-
-
-proc init*(T: type DualMessageStore, db: SqliteDatabase, capacity: int): MessageStoreResult[T] = 
-  let 
-    inmemory = StoreQueueRef.new(capacity)
-    persistent = ?SqliteStore.init(db)
-
-  info "loading messages from persistent storage to in-memory store"
-
-  let res = persistent.getAllMessages()
-  if res.isErr():
-    warn "failed to load messages from the persistent store", err = res.error
-  else: 
-    for (pubsubTopic, msg, _, storeTimestamp) in res.value:
-      discard inmemory.put(pubsubTopic, msg, computeDigest(msg), storeTimestamp)
-
-    info "successfully loaded messages from the persistent store"
-
-
-  return ok(DualMessageStore(inmemory: inmemory, persistent: persistent))
-
-
-method put*(s: DualMessageStore, pubsubTopic: string, message: WakuMessage, digest: MessageDigest, receivedTime: Timestamp): MessageStoreResult[void] =
-  ?s.inmemory.put(pubsubTopic, message, digest, receivedTime)
-  ?s.persistent.put(pubsubTopic, message, digest, receivedTime)
-  ok()
-
-method put*(s: DualMessageStore, pubsubTopic: string, message: WakuMessage): MessageStoreResult[void] =
-  procCall MessageStore(s).put(pubsubTopic, message)
-
-
-method getAllMessages*(s: DualMessageStore): MessageStoreResult[seq[MessageStoreRow]] =
-  s.inmemory.getAllMessages()
-
-
-method getMessagesByHistoryQuery*(
-  s: DualMessageStore,
-  contentTopic = none(seq[ContentTopic]),
-  pubsubTopic = none(string),
-  cursor = none(PagingIndex),
-  startTime = none(Timestamp),
-  endTime = none(Timestamp),
-  maxPageSize = MaxPageSize,
-  ascendingOrder = true
-): MessageStoreResult[seq[MessageStoreRow]] =
-  s.inmemory.getMessagesByHistoryQuery(contentTopic, pubsubTopic, cursor, startTime, endTime, maxPageSize, ascendingOrder)
-
-
-method getMessagesCount*(s: DualMessageStore): MessageStoreResult[int64] =
-  s.inmemory.getMessagesCount()
-
-method getOldestMessageTimestamp*(s: DualMessageStore): MessageStoreResult[Timestamp] =
-  s.inmemory.getOldestMessageTimestamp()
-
-method getNewestMessageTimestamp*(s: DualMessageStore): MessageStoreResult[Timestamp] =
-  s.inmemory.getNewestMessageTimestamp()
-
-
-method deleteMessagesOlderThanTimestamp*(s: DualMessageStore, ts: Timestamp): MessageStoreResult[void] =
-  # NOTE: Current in-memory store deletes messages as they are inserted. This method fails with a "not implemented" error
-  # ?s.inmemory.deleteMessagesOlderThanTimestamp(ts)
-  ?s.persistent.deleteMessagesOlderThanTimestamp(ts)
-  ok()
-
-method deleteOldestMessagesNotWithinLimit*(s: DualMessageStore, limit: int): MessageStoreResult[void] =
-  # NOTE: Current in-memory store deletes messages as they are inserted. This method fails with a "not implemented" error
-  # ?s.inmemory.deleteOldestMessagesNotWithinLimit(limit)
-  ?s.persistent.deleteOldestMessagesNotWithinLimit(limit)
-  ok()
\ No newline at end of file
diff --git a/waku/v2/node/storage/migration.nim b/waku/v2/node/storage/migration.nim
deleted file mode 100644
index 505fb75ab..000000000
--- a/waku/v2/node/storage/migration.nim
+++ /dev/null
@@ -1,81 +0,0 @@
-
-import
-  stew/results,
-  chronicles
-import
-  ../../../common/sqlite,
-  ./migration/migration_types,
-  ./migration/migration_utils
-
-export
-  migration_types,
-  migration_utils
-
-
-logScope:
-  topics = "storage.migration"
-
-
-const USER_VERSION* = 7 # increase this when there is an update in the database schema
-
-
-proc migrate*(db: SqliteDatabase, path: string, targetVersion: int64 = USER_VERSION): DatabaseResult[void] = 
-  ## Compares the user_version of the db with the targetVersion 
-  ## runs migration scripts if the user_version is outdated (does not support down migration)
-  ## path points to the directory holding the migrations scripts
-  ## once the db is updated, it sets the user_version to the tragetVersion
-  
-  # read database version
-  let userVersionRes = db.getUserVersion()
-  if userVersionRes.isErr():
-    debug "failed to get user_version", error=userVersionRes.error
-
-  let userVersion = userVersionRes.value
-
-  debug "current database user_version", userVersion=userVersion, targetVersion=targetVersion
-
-  if userVersion == targetVersion:
-    info "database is up to date"
-    return ok()
-
-  info "database user_version outdated. migrating.", userVersion=userVersion, targetVersion=targetVersion
-
-  # fetch migration scripts
-  let migrationScriptsRes = getScripts(path)
-  if migrationScriptsRes.isErr():
-    return err("failed to load migration scripts")
-
-  let migrationScripts = migrationScriptsRes.value
-
-  # filter scripts based on their versions
-  let scriptsRes = migrationScripts.filterScripts(userVersion, targetVersion)
-  if scriptsRes.isErr():
-    return err("failed to filter migration scripts")
-  
-  let scripts = scriptsRes.value
-  if scripts.len == 0:
-    return err("no suitable migration scripts")
-  
-  trace "migration scripts", scripts=scripts
-  
-  
-  # Run the migration scripts
-  for script in scripts:
-
-    for query in script.splitScript():
-      debug "executing migration statement", statement=query
-
-      let execRes = db.query(query, NoopRowHandler)
-      if execRes.isErr():
-        error "failed to execute migration statement", statement=query, error=execRes.error
-        return err("failed to execute migration statement")
-
-      debug "migration statement executed succesfully", statement=query
-    
-  # Update user_version
-  let res = db.setUserVersion(targetVersion)
-  if res.isErr():
-    return err("failed to set the new user_version")
-
-  debug "database user_version updated", userVersion=targetVersion
-  ok()
\ No newline at end of file
diff --git a/waku/v2/node/storage/migration/migration_types.nim b/waku/v2/node/storage/migration/migration_types.nim
deleted file mode 100644
index 694fd2325..000000000
--- a/waku/v2/node/storage/migration/migration_types.nim
+++ /dev/null
@@ -1,15 +0,0 @@
-{.push raises: [].}
-
-import 
-  std/[tables, os, strutils],
-  stew/results
-
-template projectRoot: string = currentSourcePath.rsplit(DirSep, 1)[0] / ".." / ".." / ".." / ".." / ".."
-const MessageStoreMigrationPath* = projectRoot / "migrations" / "message_store"
-const PeerStoreMigrationPath* = projectRoot / "migrations" / "peer_store"
-
-type MigrationScriptsResult*[T] = Result[T, string]
-type
-  MigrationScripts* = ref object of RootObj
-    migrationUp*:OrderedTable[string, string]
-    migrationDown*:OrderedTable[string, string]
\ No newline at end of file
diff --git a/waku/v2/node/storage/migration/migration_utils.nim b/waku/v2/node/storage/migration/migration_utils.nim
deleted file mode 100644
index a5d89b199..000000000
--- a/waku/v2/node/storage/migration/migration_utils.nim
+++ /dev/null
@@ -1,75 +0,0 @@
-when (NimMajor, NimMinor) < (1, 4):
-  {.push raises: [Defect].}
-else:
-  {.push raises: [].}
-
-import 
-  std/[os, algorithm, tables, strutils], 
-  chronicles, 
-  stew/results,
-  migration_types
-
-export migration_types
-
-logScope:
-  topics = "storage.migration"
-
-
-proc getScripts*(migrationPath: string): MigrationScriptsResult[MigrationScripts] =
-  ## the code in this procedure is an adaptation of https://github.com/status-im/nim-status/blob/21aebe41be03cb6450ea261793b800ed7d3e6cda/nim_status/migrations/sql_generate.nim#L4
-  var migrationScripts = MigrationScripts(migrationUp:initOrderedTable[string, string](), migrationDown:initOrderedTable[string, string]())
-  try:
-    for path in walkDirRec(migrationPath):
-      let (_, name, ext) = splitFile(path)
-      if ext != ".sql": continue
-
-      let parts = name.split(".")
-      if parts.len < 2:
-        continue
-      let script = parts[0]
-      let direction = parts[1]
-
-      debug "name", script=script
-      case direction:
-      of "up":
-        migrationScripts.migrationUp[script] = readFile(path)
-        debug "up script", readScript=migrationScripts.migrationUp[script]
-      of "down":
-        migrationScripts.migrationDown[script] = readFile(path)
-        debug "down script", readScript=migrationScripts.migrationDown[script]
-      else:
-        debug "Invalid script: ", name
-
-    migrationScripts.migrationUp.sort(system.cmp)
-    migrationScripts.migrationDown.sort(system.cmp)
-  
-    ok(migrationScripts)
-
-  except OSError, IOError:
-    debug "failed to load the migration scripts"
-    return err("failed to load the migration scripts") 
-
-
-proc filterScripts*(migrationScripts: MigrationScripts, s: int64, e: int64 ): Result[seq[string], string] = 
-  ## returns migration scripts whose version fall between s and e (e is inclusive)
-  var scripts: seq[string]
-  try:
-    for name, script in migrationScripts.migrationUp:
-      let parts = name.split("_")
-      #TODO this should be int64
-      let ver = parseInt(parts[0])
-      # filter scripts based on their version
-      if s < ver and ver <= e:
-        scripts.add(script)
-    ok(scripts)
-  except ValueError:
-    return err("failed to filter scripts")
-
-proc splitScript*(script: string): seq[string] =
-  ## parses the script into its  individual sql commands and returns them
-  var queries: seq[string] = @[]
-  for q in script.split(';'):
-    if  isEmptyOrWhitespace(q): continue
-    let query = q.strip() & ";"
-    queries.add(query)
-  return queries
diff --git a/waku/v2/node/waku_node.nim b/waku/v2/node/waku_node.nim
index 9cb12f5d2..dd13e4e9f 100644
--- a/waku/v2/node/waku_node.nim
+++ b/waku/v2/node/waku_node.nim
@@ -36,10 +36,10 @@ import
   ../utils/peers, 
   ../utils/wakuenr,
   ./peer_manager/peer_manager,
-  ./storage/message/waku_store_queue,
-  ./storage/message/message_retention_policy,
-  ./storage/message/message_retention_policy_capacity,
-  ./storage/message/message_retention_policy_time,
+  ./message_store/waku_store_queue,
+  ./message_store/message_retention_policy,
+  ./message_store/message_retention_policy_capacity,
+  ./message_store/message_retention_policy_time,
   ./dnsdisc/waku_dnsdisc,
   ./discv5/waku_discv5,
   ./wakuswitch
diff --git a/waku/v2/protocol/waku_store/protocol.nim b/waku/v2/protocol/waku_store/protocol.nim
index a9e3c84e5..90707aa2b 100644
--- a/waku/v2/protocol/waku_store/protocol.nim
+++ b/waku/v2/protocol/waku_store/protocol.nim
@@ -18,8 +18,8 @@ import
   libp2p/stream/connection,
   metrics
 import
-  ../../node/storage/message/message_retention_policy,
-  ../../node/storage/message/waku_store_queue,
+  ../../node/message_store/message_retention_policy,
+  ../../node/message_store/waku_store_queue,
   ../../node/peer_manager/peer_manager,
   ../../utils/time,
   ../waku_message,