Food processing transforms the physical and chemical properties of food, potentially modifying their effect on gut microbiota composition and functionality. This chapter explores how thermal food processing methods, both at the household and industrial levels, impact the gut microbiota. Research shows that the impact of thermal processing strongly depends on the food type, thermal processing method, and specific measurements of composition and functionality. For gut microbiota composition and short-chain fatty acid (SCFA) production, thermal processing tends to have a more positive effect on carbohydrate-rich foods, while lipid-rich foods yield the least favorable outcomes. Thermal processing also shows positive effects on the bioaccessibility and microbial metabolism of (poly)phenols. Thermal processing can also enhance the gut microbiota’s ability to improve the bioaccessibility of minerals and carotenoids, though it is generally detrimental to the release of antioxidant capacity. Microwaving has proven to be one of the most effective thermal processing methods for promoting gut microbiota composition and functionality. The effect of compounds generated during thermal processing (e.g., Maillard reaction products) on the gut microbiota remains inconclusive. Thermal food processing could also be a key factor to consider in personalized nutrition for enhancing the composition and functionality of the gut microbiota at the individual level.