diff --git a/src/Chaptarr.Core.Test/Datastore/ExtraFileAuthorBookIndexMigrationFixture.cs b/src/Chaptarr.Core.Test/Datastore/ExtraFileAuthorBookIndexMigrationFixture.cs
new file mode 100644
index 00000000..b4dddcb2
--- /dev/null
+++ b/src/Chaptarr.Core.Test/Datastore/ExtraFileAuthorBookIndexMigrationFixture.cs
@@ -0,0 +1,135 @@
+using System;
+using System.IO;
+using System.Linq;
+using Dapper;
+using Microsoft.Data.Sqlite;
+using NLog;
+using NUnit.Framework;
+using NzbDrone.Core.Datastore;
+using NzbDrone.Core.Datastore.Migration.Framework;
+
+namespace Chaptarr.Core.Test.Datastore
+{
+    [TestFixture]
+    public class ExtraFileAuthorBookIndexMigrationFixture
+    {
+        private string _databasePath;
+        private string _connectionString;
+        private SqliteConnection _connection;
+
+        [SetUp]
+        public void SetUp()
+        {
+            _databasePath = Path.Combine(TestContext.CurrentContext.WorkDirectory, $"extra_file_index_{Guid.NewGuid():N}.db");
+            _connectionString = new SqliteConnectionStringBuilder
+            {
+                DataSource = _databasePath,
+                Mode = SqliteOpenMode.ReadWriteCreate,
+                Pooling = false
+            }.ToString();
+
+            _connection = new SqliteConnection(_connectionString);
+            _connection.Open();
+            _connection.Execute(@"
+                CREATE TABLE ""VersionInfo"" (
+                    ""Version"" INTEGER PRIMARY KEY,
+                    ""AppliedOn"" TEXT NULL,
+                    ""Description"" TEXT NULL
+                );
+                WITH RECURSIVE versions(version) AS
+                (
+                    SELECT 1
+                    UNION ALL
+                    SELECT version + 1 FROM versions WHERE version < 109
+                )
+                INSERT INTO ""VersionInfo"" (""Version"", ""AppliedOn"", ""Description"")
+                SELECT version, CURRENT_TIMESTAMP, 'test baseline' FROM versions;
+            ");
+        }
+
+        [TearDown]
+        public void TearDown()
+        {
+            _connection?.Dispose();
+            SqliteConnection.ClearAllPools();
+
+            if (File.Exists(_databasePath))
+            {
+                File.Delete(_databasePath);
+            }
+        }
+
+        private void Migrate()
+        {
+            var migrationController = new MigrationController(LogManager.GetLogger("ExtraFileAuthorBookIndexMigrationFixture"), null);
+            migrationController.Migrate(_connectionString, new MigrationContext(MigrationType.Main, 110), DatabaseType.SQLite);
+        }
+
+        private string[] IndexColumns(string tableName, string indexName)
+        {
+            var exists = _connection.QuerySingle<int>($"SELECT COUNT(*) FROM pragma_index_list('{tableName}') WHERE name = '{indexName}';");
+            return exists == 0
+                ? Array.Empty<string>()
+                : _connection.Query<string>($"SELECT name FROM pragma_index_info('{indexName}') ORDER BY seqno;").ToArray();
+        }
+
+        [Test]
+        public void should_index_author_and_book_on_both_extra_file_tables_in_query_order()
+        {
+            _connection.Execute(@"
+                CREATE TABLE ""MetadataFiles"" (""Id"" INTEGER PRIMARY KEY, ""AuthorId"" INTEGER NOT NULL, ""BookId"" INTEGER NULL);
+                CREATE TABLE ""ExtraFiles"" (""Id"" INTEGER PRIMARY KEY, ""AuthorId"" INTEGER NOT NULL, ""BookId"" INTEGER NULL);");
+
+            Migrate();
+
+            Assert.Multiple(() =>
+            {
+                Assert.That(IndexColumns("MetadataFiles", "IX_MetadataFiles_AuthorId_BookId"), Is.EqualTo(new[] { "AuthorId", "BookId" }));
+                Assert.That(IndexColumns("ExtraFiles", "IX_ExtraFiles_AuthorId_BookId"), Is.EqualTo(new[] { "AuthorId", "BookId" }));
+            });
+        }
+
+        [Test]
+        public void should_make_the_per_book_delete_use_the_index_instead_of_scanning()
+        {
+            _connection.Execute(@"CREATE TABLE ""MetadataFiles"" (""Id"" INTEGER PRIMARY KEY, ""AuthorId"" INTEGER NOT NULL, ""BookId"" INTEGER NULL);");
+
+            Migrate();
+
+            Assert.That(IndexColumns("MetadataFiles", "IX_MetadataFiles_AuthorId_BookId"), Is.EqualTo(new[] { "AuthorId", "BookId" }));
+
+            // A fresh connection: the migration ran on its own connection, and a connection opened before
+            // it keeps planning against the schema it saw then.
+            using var fresh = new SqliteConnection(_connectionString);
+            fresh.Open();
+
+            // EXPLAIN QUERY PLAN returns (id, parent, notused, detail); the detail column names the access path.
+            var plan = string.Join(" | ", fresh.Query(
+                @"EXPLAIN QUERY PLAN DELETE FROM ""MetadataFiles"" WHERE ""AuthorId"" = 1 AND ""BookId"" = 2;")
+                .Select(row => (string)row.detail));
+
+            Assert.That(plan, Does.Contain("IX_MetadataFiles_AuthorId_BookId"), "the delete must be planned as an index search, not a table scan");
+        }
+
+        [Test]
+        public void should_tolerate_missing_tables_and_missing_columns()
+        {
+            // ExtraFiles present but without the columns (older/odd schema): nothing to index, must not throw.
+            _connection.Execute(@"CREATE TABLE ""ExtraFiles"" (""Id"" INTEGER PRIMARY KEY, ""Path"" TEXT NULL);");
+
+            Assert.DoesNotThrow(Migrate);
+            Assert.That(IndexColumns("ExtraFiles", "IX_ExtraFiles_AuthorId_BookId"), Is.Empty);
+        }
+
+        [Test]
+        public void should_not_fail_when_the_index_already_exists()
+        {
+            _connection.Execute(@"
+                CREATE TABLE ""MetadataFiles"" (""Id"" INTEGER PRIMARY KEY, ""AuthorId"" INTEGER NOT NULL, ""BookId"" INTEGER NULL);
+                CREATE INDEX ""IX_MetadataFiles_AuthorId_BookId"" ON ""MetadataFiles"" (""AuthorId"", ""BookId"");");
+
+            Assert.DoesNotThrow(Migrate);
+            Assert.That(IndexColumns("MetadataFiles", "IX_MetadataFiles_AuthorId_BookId"), Is.EqualTo(new[] { "AuthorId", "BookId" }));
+        }
+    }
+}
diff --git a/src/NzbDrone.Core/Datastore/Migration/110_add_extra_file_author_book_indexes.cs b/src/NzbDrone.Core/Datastore/Migration/110_add_extra_file_author_book_indexes.cs
new file mode 100644
index 00000000..7042a6de
--- /dev/null
+++ b/src/NzbDrone.Core/Datastore/Migration/110_add_extra_file_author_book_indexes.cs
@@ -0,0 +1,36 @@
+using FluentMigrator;
+using NzbDrone.Core.Datastore.Migration.Framework;
+
+namespace NzbDrone.Core.Datastore.Migration
+{
+    // ExtraFileService<T> looks its rows up (GetFilesByBook) and deletes them (DeleteForBook, run once per
+    // deleted book by every BookDeletedEvent) with WHERE "AuthorId" = @a AND "BookId" = @b. Neither table
+    // had an index on those columns, so each lookup/delete was a sequential scan: ~5 ms against
+    // MetadataFiles at ~70k rows, which made it the single most expensive statement of an author refresh
+    // that prunes books (a book deletion costs ~0.1 ms everywhere else on the delete path).
+    [Migration(110)]
+    public class add_extra_file_author_book_indexes : NzbDroneMigrationBase
+    {
+        protected override void MainDbUpgrade()
+        {
+            AddIndex("MetadataFiles", "IX_MetadataFiles_AuthorId_BookId");
+            AddIndex("ExtraFiles", "IX_ExtraFiles_AuthorId_BookId");
+        }
+
+        private void AddIndex(string tableName, string indexName)
+        {
+            if (!Schema.Table(tableName).Exists() ||
+                !Schema.Table(tableName).Column("AuthorId").Exists() ||
+                !Schema.Table(tableName).Column("BookId").Exists() ||
+                Schema.Table(tableName).Index(indexName).Exists())
+            {
+                return;
+            }
+
+            Create.Index(indexName)
+                .OnTable(tableName)
+                .OnColumn("AuthorId").Ascending()
+                .OnColumn("BookId").Ascending();
+        }
+    }
+}