diff --git a/data/src/main/java/tachiyomi/data/category/CategoryRepositoryImpl.kt b/data/src/main/java/tachiyomi/data/category/CategoryRepositoryImpl.kt
index 729703d54..c60fd9daa 100644
--- a/data/src/main/java/tachiyomi/data/category/CategoryRepositoryImpl.kt
+++ b/data/src/main/java/tachiyomi/data/category/CategoryRepositoryImpl.kt
@@ -77,6 +77,9 @@ class CategoryRepositoryImpl(
 
     override suspend fun updateAllOrders(orderedIds: List<Long>) {
         database.transaction {
+            orderedIds.forEachIndexed { index, categoryId ->
+                database.categoriesQueries.updateOrder(order = -index - 2L, categoryId = categoryId)
+            }
             orderedIds.forEachIndexed { index, categoryId ->
                 database.categoriesQueries.updateOrder(order = index.toLong(), categoryId = categoryId)
             }
diff --git a/domain/src/main/java/tachiyomi/domain/category/interactor/DeleteCategory.kt b/domain/src/main/java/tachiyomi/domain/category/interactor/DeleteCategory.kt
index bbdbe3b7d..71050a5d6 100644
--- a/domain/src/main/java/tachiyomi/domain/category/interactor/DeleteCategory.kt
+++ b/domain/src/main/java/tachiyomi/domain/category/interactor/DeleteCategory.kt
@@ -4,6 +4,7 @@ import dev.zacsweers.metro.Inject
 import logcat.LogPriority
 import tachiyomi.core.common.util.lang.withNonCancellableContext
 import tachiyomi.core.common.util.system.logcat
+import tachiyomi.domain.category.model.Category
 import tachiyomi.domain.category.repository.CategoryRepository
 import tachiyomi.domain.download.service.DownloadPreferences
 import tachiyomi.domain.library.service.LibraryPreferences
@@ -23,7 +24,9 @@ class DeleteCategory(
             return@withNonCancellableContext Result.InternalError(e)
         }
 
-        val orderedIds = categoryRepository.getAll().map { it.id }
+        val orderedIds = categoryRepository.getAll()
+            .filterNot(Category::isSystemCategory)
+            .map { it.id }
 
         val defaultCategory = libraryPreferences.defaultCategory.get()
         if (defaultCategory == categoryId.toInt()) {