diff --git a/internal/praefect/datastore/migrations/20210906145021_link_repository_id.go b/internal/praefect/datastore/migrations/20210906145021_link_repository_id.go
new file mode 100644
index 0000000000000000000000000000000000000000..08c9663bddd70bf026af2f00c7272e0d77f74f6b
--- /dev/null
+++ b/internal/praefect/datastore/migrations/20210906145021_link_repository_id.go
@@ -0,0 +1,28 @@
+package migrations
+
+import migrate "github.com/rubenv/sql-migrate"
+
+func init() {
+	m := &migrate.Migration{
+		Id: "20210906145021_link_repository_id",
+		Up: []string{
+			`
+UPDATE storage_repositories
+SET repository_id = repositories.repository_id
+FROM repositories
+WHERE storage_repositories.virtual_storage = repositories.virtual_storage
+AND   storage_repositories.relative_path   = repositories.relative_path
+			`,
+			`
+UPDATE repository_assignments
+SET repository_id = repositories.repository_id
+FROM repositories
+WHERE repository_assignments.virtual_storage = repositories.virtual_storage
+AND   repository_assignments.relative_path   = repositories.relative_path
+			`,
+		},
+		Down: []string{},
+	}
+
+	allMigrations = append(allMigrations, m)
+}
diff --git a/internal/praefect/datastore/migrations/20210921131816_backfill_replica_path.go b/internal/praefect/datastore/migrations/20210921131816_backfill_replica_path.go
new file mode 100644
index 0000000000000000000000000000000000000000..e18ea3d4c66bacb2fe7740ece5ce1b38d28084e6
--- /dev/null
+++ b/internal/praefect/datastore/migrations/20210921131816_backfill_replica_path.go
@@ -0,0 +1,13 @@
+package migrations
+
+import migrate "github.com/rubenv/sql-migrate"
+
+func init() {
+	m := &migrate.Migration{
+		Id:   "20210921131816_backfill_replica_path",
+		Up:   []string{"UPDATE repositories SET replica_path = relative_path"},
+		Down: []string{},
+	}
+
+	allMigrations = append(allMigrations, m)
+}
diff --git a/internal/praefect/datastore/migrations/20210922091614_repository_id_primary_key_indexes.go b/internal/praefect/datastore/migrations/20210922091614_repository_id_primary_key_indexes.go
new file mode 100644
index 0000000000000000000000000000000000000000..e5441ff9482dfb8e75a160211f4b5019ccd919d0
--- /dev/null
+++ b/internal/praefect/datastore/migrations/20210922091614_repository_id_primary_key_indexes.go
@@ -0,0 +1,19 @@
+package migrations
+
+import migrate "github.com/rubenv/sql-migrate"
+
+func init() {
+	m := &migrate.Migration{
+		Id: "20210922091614_repository_id_primary_key_indexes",
+		Up: []string{
+			"CREATE UNIQUE INDEX repository_assignments_new_pkey ON repository_assignments (repository_id, storage)",
+			"CREATE UNIQUE INDEX storage_repositories_new_pkey ON storage_repositories (repository_id, storage)",
+		},
+		Down: []string{
+			"DROP INDEX repository_assignments_new_pkey",
+			"DROP INDEX storage_repositories_new_pkey",
+		},
+	}
+
+	allMigrations = append(allMigrations, m)
+}