Coastal ecosystems dominate oceanic methane (CH₄) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH₄ oxidizing bacteria) drive the spatial–temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH₄ sediment–water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH₄. We show that macrofauna increases CH₄ fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH₄ flux reduces CH₄ pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH₄ emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.