The effects of wavy channels upon steam methane reforming in catalytic micro-structured reactors, using Nickle as the catalyst, are investigated numerically. Laminar, three-dimensional models of reacting flows, with heterogeneous chemistry, are developed and applied to micro-structured reactors with different wave patterns on their internal walls. It is observed that introduction of surface waves on the walls of reactor, can significantly alter production and consumption of H2 and CH4. This is shown to be due to large fluctuations in convective mass and heat transfer, induced by the surface waviness. In particular, it is shown that separation and reattachment of concentration and thermal boundary layers and the subsequent modifications in Sherwood and Nusselt number can significantly affect the catalytic processes over the walls of reactor. A major local intensification of catalytic processes is observed where Sherwood and Nusselt number are maximised. Similarly, the catalytic process becomes highly inefficient in places with minimal Sherwood (and Nusselt) number. The analyses further reveal that a strategic discrete coating of wavy walls with the catalyst can substantially improve the performance of microstructure. For example, by coating only 25% of the surface area of wavy walls, CH4 conversion rate and selectivity per coated surface area increase by 459% and 308% compared to those of an equivalent fully coated straight channel. This implies the possibility of developing highly efficient and cost-effective catalytic micro-reactors for production of hydrogen from methane.