Areas of char or overcooking commonly appear in foods people consume. It has been reported that overcooked food is harmful to human health. However, little research exists on the effect of overcooking on digestible protein and starch content and gut microbial fermentation. This study aimed to reveal the connection between overcooking and the content of digestible protein and starch, as well as its impact on gut microbial fermentation. Digestible protein in the standard cooked ground beef patty was significantly higher than the overcooked samples (p = 0.009). Standard-cooked whole wheat bread also showed a significantly higher digestible protein content compared with overcooked (p = 0.009). A significant difference was also found in digestible starch content between standard cooked and overcooked bread samples (p = 0.02). Overcooking decreased acetate, propionate, iso-butyrate, iso-valerate and ammonia production by the gut microbiota during fermentation of the beef sample, and decreased propionate and ammonia production during fermentation of the bread sample (p < 0.05). Interestingly, overcooking enhanced butyrate production by the microbiota during fermentation of the bread sample (24 h of fermentation, p < 0.001; 48 h of fermentation, p = 0.02), while no significant difference was found between overcooked and standard cooked beef samples (24 h of fermentation, p = 0.15; 48 h of fermentation, p = 0.4). Overcooking resulted in reductions in many Pseudomonadota and favored several Bacillota, especially Ruminococcaceae and Oscillospiraceae, which contain butyrate producers. Overall, overcooking reduced digestible protein, digestible starch, and fermentation of proteins. Unexpectedly, overcooking induced several purportedly favorable effects on the gut microbiota due to the decreased protein fermentation, which, in future studies, should be weighed against the previous reports that overcooking is deleterious to human health.