Soil microbial communities are essential to ecosystem function, particularly in tropical agroforestry systems where land-use changes and fertilizer inputs can significantly alter soil health. Despite the increasing adoption of coffee agroforestry as a sustainable land management strategy, the specific impacts of different fertilizer types on soil bacterial diversity and quality remain insufficiently explored. This study aimed to assess how organic, inorganic, and mixed fertilizer treatments affect soil bacterial community structure and soil quality in a coffee agroforestry system in UB Forest, Indonesia, compared to an undisturbed protected area. Soil samples were collected three months post-fertilization and analyzed using next-generation sequencing to determine bacterial community structure and diversity indices. Soil chemical parameters were also assessed. Results showed that mixed fertilizer (MF) treatments enhanced soil total nitrogen, microbial population, and overall diversity, while organic fertilizer (OF) promoted higher bacterial richness and evenness. Inorganic fertilizer (IF) increased nutrient-specific bacterial populations but reduced overall diversity. Protected areas (PA) had high organic content but comparatively lower microbial diversity, possibly due to limited nutrient input and recalcitrant organic compounds. Principal Component Analysis revealed strong positive correlations between MF treatment and microbial and soil health indicators. This study demonstrates that combining organic and inorganic fertilizers optimizes microbial diversity and soil function, supporting more resilient and productive agroecosystems. Conversely, exclusive reliance on inorganic fertilizers may compromise microbial balance and long-term soil health.