Everyday dietary decisions have important short-term and long-term consequences for health and well-being. How do we decide what to eat, and what physiological and neurobiological systems are involved in those decisions? Here, we integrate findings from thus-far separate literatures: (a) the cognitive neuroscience of dietary decision-making, and (b) growing evidence of gut-brain interactions and especially influences of the gut microbiome on diet and health outcomes. We review findings that suggest that dietary decisions and food consumption influence nutrient sensing, homeostatic signaling in the gut, and the composition of the gut microbiome. In turn, the microbiome can influence host health and behavior. Through reward signaling pathways, the microbiome could potentially affect food and drink decisions. Such bidirectional links between gut microbiome and the brain systems underlying dietary decision-making may lead to self-reinforcing feedback loops that determine long-term dietary patterns, body mass, and health outcomes. This article is categorized under: Economics > Individual Decision-Making Psychology > Brain Function and Dysfunction Psychology > Reasoning and Decision Making.