Specify a primary key for every table using the most frequently queried column or columns, or an auto-increment value if there is no obvious primary key.

Use joins wherever data is pulled from multiple tables based on identical ID values from those tables. For fast join performance, define foreign keys on the join columns, and declare those columns with the same data type in each table. Adding foreign keys ensures that referenced columns are indexed, which can improve performance. Foreign keys also propagate deletes and updates to all affected tables, and prevent insertion of data in a child table if the corresponding IDs are not present in the parent table.

Turn off autocommit. Committing hundreds of times a second puts a cap on performance (limited by the write speed of your storage device).

Group sets of related DML operations into transactions by bracketing them with START TRANSACTION and COMMIT statements. While you don't want to commit too often, you also don't want to issue huge batches of INSERT, UPDATE, or DELETE statements that run for hours without committing.

Do not use LOCK TABLES statements. InnoDB can handle multiple sessions all reading and writing to the same table at once without sacrificing reliability or high performance. To get exclusive write access to a set of rows, use the SELECT ... FOR UPDATE syntax to lock just the rows you intend to update.

Enable the innodb_file_per_table variable or use general tablespaces to put the data and indexes for tables into separate files instead of the system tablespace. The innodb_file_per_table variable is enabled by default.

Evaluate whether your data and access patterns benefit from the InnoDB table or page compression features. You can compress InnoDB tables without sacrificing read/write capability.

Run the server with the --sql_mode=NO_ENGINE_SUBSTITUTION option to prevent tables from being created with storage engines that you do not want to use.