Given the increasing worldwide prevalence of obesity and associated metabolic disturbances, novel therapeutic strategies are imperatively required. A plausible manner to increase energy expenditure is the enhancement of thermogenic pathways in white (WAT) and brown adipose tissue (BAT). In the last 15 years, the identification of novel endogenous mechanisms to promote BAT activity or browning of WAT has pointed at gut microbiota as an important modulator of host metabolic homeostasis and energy balance. In this review, we focused on the relationship between gut microbiota composition and adipose tissue thermogenic program (including BAT activity and browning of WAT) in both physiological and stress conditions. Specifically, we reviewed the effects of fasting, caloric restriction, cold stress and metabolic endotoxemia on both browning and gut microbiota shifts. Mechanistically speaking, processes related to bile acid metabolism and the endocannabinoid system seem to play an important role. In summary, the gut microbiota seems to impact WAT and BAT physiology at multiple levels.