Although various studies have been conducted in screening oil-degrading microorganisms and the macro-scale degrading efficiency, critical processes of microorganisms in the microscale porous space are not clear, which are important for microbial enhanced oil recovery (MEOR) and bioremediation of oil contaminated environments. In this work a gas-permeable microchannel filled with crude oil was employed to study the microbial processes in a microscale environment. Cells of a petroleum-degrading Dietzia strain were suspended with two different media and the resulting suspensions were ejected into the microchannel. The degradation processes in the oil–suspension system were then analyzed. The changes in the behavior of the cells and the variation of the oil–suspension interface as well as the evolution of the suspension patterns and structures were observed. ‘Aggregates’, ‘clustered cells’, and ‘oil droplets’ were characteristically formed in comparison with the control experiments. Oil droplets were formed at the oil–suspension interface and dispersed into the suspension, and this process could be drastic that a plume of oil droplets was issuing into the suspension. All the changes could be attributed to the degradation of crude oil by the cells and the production of biosurfactants which could reduce the interface tension and increase the dissolution of the crude oil. The present work is a preliminary step toward a comprehensive understanding of microbial process in microscale porous space.