Coffee agroforestry has become a land use system that provides both ecological and economic benefits, so it is managed in various ways. Pruning and fertilizer management is a combination that is applied for optimal production. However, understanding the effect of combined management on soil respiration and functional microbial populations remains unclear. This study aimed to determine the effect of combining pruning and fertilizer management on soil respiration and functional bacterial populations as well as to elucidate the relationship between tested parameters. The study was conducted in UB Forest. A factorial randomized block design consisting of three factors, i.e., coffee pruning, type of fertilizer, and fertilizer doses was used. The results showed that combining three factors affected the diazotrophic bacterial population and soil respiration, which is sensitive to management changes. Coffee pruning and mixed fertilizer (inorganic + organic) application affected soil respiration and microbial populations, while the dose affected each parameter differently. The conducted study suggests that pruning management with mixed fertilizer application can substitute inorganic fertilizer as more environmentally sustainable management in coffee-based agroforestry.