An integrated biomass conversion system and a method of starting and shutting down the system are disclosed. The integrated biomass conversion system comprises a syngas generator, such as a gasifier, a cleanup engine and a syngas utilization system, which could be a power producing engine or a chemical reactor for chemical or fuel synthesis. The cleanup engine operates rich and at high temperatures so that the tars exhausted by the syngas generators are destroyed and not allowed to foul other components. An orderly sequence to start and shut down the integrated biomass conversion system is disclosed.