Gene regulatory networks allow single cells to adopt a wide range of different phenotypes in response to changes in environmental conditions. The ecological implications of these cellular computations are poorly understood, and they are largely absent from models of microbial community assembly. Here, we highlight a number of examples where ecological interactions are or may be affected by cellular computations. Our review identifies specific opportunities for integrating cellular decision-making into mathematical models of microbe-microbe interactions and community assembly. We argue that incorporating cellular decision-making into microbial ecology will be critical in order to gain a quantitative understanding of microbial biogeography.