Agroforestry systems (AFSs) are considered sustainable forms of land management, but their impact on soil microbial biodiversity remains poorly understood. Here, we compared the structure and diversity of bacterial communities in rubber-based AFSs in tropical China that had different management types and stand ages: 10 year-old rubber mono- (YR) and intercropping (YRF), and 22-year-old rubber mono- (MR) and intercropping (MRF). Stand age had a stronger effect on bacterial communities than management type or season. Compared to the corresponding monocultures, YRF maintained bacterial diversity despite experiencing a decrease in abundance, especially at soil depths of 0-5 and 5-30 cm, whereas MRF enhanced bacterial diversity with a consistent abundance. Bacterial communities in AFSs exhibited obvious horizon-specific seasonal variations due to spatial and temporal heterogeneity in edaphic factors. Acidobacteria, Proteobacteria and Actinobacteria were the most dominant bacterial phyla in tropical AFSs in China, while Kitasatospora, Streptomyces, Nitrospira, Bacillus and Pseudomonas were the key genera. Soil pH, available phosphorus and dissolved organic nitrogen emerged as the major drivers of these bacterial community patterns. These findings indicate that the establishment of rubber based AFSs, particularly those in mature stands, is a promising management practice for alleviating the adverse effects of rubber monoculture on bacterial biodiversity, including severe acidification and nutrient depletion. Our study highlights the importance of considering multiple effects when investigating bacterial communities in AFSs under climate change scenarios.