In the present case study, the gut microbiota (GM) profile of a male elite mountain runner (34 years, 171 cm, 59 kg, VO_2max = 92 mL/min/kg) was analyzed over a 5-month competitive period (6 samples). Gut microbiota diversity increased throughout the season, where higher levels coincided with peak performance, and shorter and longer races (42 km versus 172 km) produced different phenotypic GM changes. Shorter races promoted elevation of protective bacteria related to positive benefits (higher production of short-chain fatty acids, lactate resynthesis, and mucin degraders). By contrast, longer races promoted an elevation of opportunistic pathogenic bacteria while reducing protective commensal bacteria. The present findings indicate that a higher resilience of the GM after competitions may support rapid recovery from maximal exercise. Gut microbiota analyses before and after competition could represent a rapid indicator for the (patho) physiological impact of exercise and provide information on gut health and the recovery time needed.