Anaerobic digestion (AD) is a promising technology to process protein-rich wastewater. However, incomplete protein degradation during the acidification of organic matter is frequently observed when carbohydrates are present. Literature reports little information to explain the mechanisms behind this phenomenon. This MSc study investigated the relationship between microbial composition and the negative effect of carbohydrates on anaerobic protein degradation in the acid-phase by restricting the carbon source to a mixed culture in a continuously stirred tank anaerobic reactor. Two continuously stirred anaerobic reactors fed with restrictive protein and/or carbohydrate substrates were operated and compared in the aspects of acidification, deamination, protease activity, and microbial composition. Results showed that the deamination degree in the protein-feeding reactor decreased from 77% to 15% and the acidification degree decreased from 75% to 34% when the restrictive carbon source shifted from proteins to mixtures of proteins and carbohydrates. A decrease in protease activity was also observed. Anaerobic protein degradation was significantly retarded by the presence of carbohydrates. Results of the microbial composition analysis showed that generalists (i.e. microorganisms that can ferment both proteins and carbohydrates) that preferentially consumed carbohydrates were the predominant populations in the microbial community when carbohydrates were present as additional substrates. Therefore, the observed negative effect of carbohydrates on protein degradation in acid-phase could be mainly attributed to the preferential substrate utilization feature of generalists. Further research on the metabolism functional analysis of the microbial community should be employed to confirm this hypothesis. Overall, this study offers a better understanding of the mechanisms behind the negative effect of carbohydrates on protein degradation, which can provide some hints of the design of the anaerobic digestion process of protein-rich wastewater.