Physical ecosystem engineers are organisms that physically modify the abiotic environment. They can affect biogeochemical processing by changing the availability of resources for microbes (e.g., carbon, nutrients) or by changing abiotic conditions affecting microbial process rates (e.g., soil moisture or temperature). Physical ecosystem engineers can therefore create biogeochemical heterogeneity in soils and sediments. They do so via general mechanisms influencing the flows of materials (i.e., modification of fluid dynamic properties, fluid pumping, and material transport) or the transfer of heat (i.e., modification of heat transfer properties, direct heat transfer, and convective forcing). The consequences of physical ecosystem engineering for biogeochemical processes can be predicted by considering the resources or abiotic conditions that limit or promote a reaction, and the effect of physical ecosystem engineering on these resources or abiotic conditions via the control they exert on material flows and heat transfer.