In this paper, recent achievements in the application of the lattice Boltzmann method (LBM) to complex fluid flows are reported. More specifically, we focus on flows through reactive porous media, such as the flow through the substrate of a selective catalytic reactor (SCR) for the reduction of gaseous pollutants in the automotive field; pulsed-flow analysis through heterogeneous catalyst architectures; and transport and electro-chemical phenomena in microbial fuel cells (MFC) for novel waste-to-energy applications. To the authors’ knowledge, this is the first known application of LBM modeling to the study of MFCs, which represents by itself a highly innovative and challenging research area. The results discussed here essentially confirm the capabilities of the LBM approach as a flexible and accurate computational tool for the simulation of complex multi-physics phenomena of scientific and technological interest, across physical scales.