A method, system and computer program product for processing queries in a hybrid database system. A database management system of the hybrid database system obtains an estimated execution time of a query by an online transaction processing engine. The database management system further obtains an estimated execution time of the query by a database accelerator. Furthermore, the database management system determines a wait time (which could be zero) for the database accelerator to process the query. The database management system then determines whether the online transaction processing engine or the database accelerator will process the query using the estimated execution time of the query by the online transaction processing engine, the estimated execution time of the query by the database accelerator and the wait time (which could be zero) for the database accelerator to process the query. In this manner, the processing of queries in hybrid database systems is optimized.