© 2017 Elsevier B.V. Agricultural practices, such as crop residue management and tillage, change biological, physical and chemical soil characteristics. The aim of this study was to investigate the effect of the application of bean plant residue (Phaseolus vulgaris L.), one of the major crops in Mexico, on the bacterial community structure in soil cultivated conventionally (conventional beds, CB) or under a conservation agriculture system (permanent beds, PB) and compared it to the effect of maize plant residue application. Soil samples were incubated aerobically at ambient temperature (22 ± 2 °C) for 56 days. The bacterial community in the unamended PB soil was significantly different from that in the unamended CB soil, e.g. Acidobacteria, PB > CB, while Actinobacteria PB < CB. Considering no priming effect, 44% of the applied bean plant residue was mineralized in the PB soil after 56 days and 78% in CB soil, while mineral N increased by 7.9 mg kg−1 in both the PB and the CB soil. Bacillus, Micrococcaceae and Streptomyces were the first most abundant degraders of the bean plant residue. They continued to participate in the degradation of the bean plant residue and/or its metabolic products until day 7 (Micrococcaceae) or day 28 (Bacillus and Streptomyces). Actinobacteria and TM7, known copiotrophs, were the most abundant after harvest while Planctomycetes and Verrucomicrobia, known oligotrophs, during the growing season. It was found that agricultural practices had a significant effect on the bacterial community structure and bean plant residue was degraded primarily by phylotypes belonging to Bacillus, Micrococcaceae and Streptomyces. Further research is needed to improve our knowledge on how changes in microbial community structures alter plant nutrient cycling.