Since the introduction of microchemical systems (MCS) in the last decade, it has been recognized that one of the most crucial challenges is the implementation of an appropriate control strategy. A novel study in realizing a controllable miniature chemical plant for a small-scale hydrogen source for fuel cells is presented. Catalytic steam reforming (SR) reaction of a methanol–water mixture was the model reaction studied. A microscaled reactor, sensors and actuators, were successfully prepared and integrated by using microelectromechanical systems (MEMS) technology. Microfabricated system components were then interconnected with a comprehensive control algorithm which could form the basis for an eventual autonomous, self-contained system. MCS represent a concept wherein precisely microfabricated fluid passages and reaction zones are integrated with sensors and actuators. Having an appropriate control strategy for the entire system of MCS is therefore a significant technical challenge. Although numerous MEMS-based examples of sensors and actuators exist for control of pressure, temperature and flow, there are few cases where these components have been combined with chemical reaction units and control algorithms into MCS. In this study, control of temperature and flow allows the hydrogen production rate to be modulated in a suitable fashion to support proton exchange fuel cell operation as a model. The reaction characteristics with temperature and flow changes, cold start-up behavior and the response to rapid changes in hydrogen demand were investigated. The control scheme implemented showed potential for autonomous control of fuel processing and other microchemical processing applications.