Biochar-based fertilizers have the potential to improve soil quality by enhancing soil microbial communities, yet their direct effects on crop yield and quality are not well understood. To address this gap, we conducted a pot-based field study to evaluate the impact of traditional chemical fertilizers alone, traditional fertilizers supplemented with biochar, and biochar-based fertilizers on soil properties and bacterial communities. We also investigated how these treatments affected tobacco (Nicotiana tabacum) yield and leaf aroma quality. Biochar-based fertilizers increased soil carbon (C) and nitrogen (N) pools compared to the control, leading to greater bacterial diversity and richness. Consequently, tobacco biomass increased from 449 g/pot to 517 g/pot, and leaf aroma content rose from 625 µg/g to 832 µg/g. Linear discriminant analysis and partial least squares path modeling identified 13 key bacterial phylotypes, including plant growth-promoting bacteria (PGPB) such as Burkholderiaceae, Novosphingobium, Bacillus, Chitinophagaceae, Sphingomonas, Acidobacteriaceae, Acidobacteria, and Flavobacterium, that positively influenced tobacco leaf aroma constituents. Our findings suggest that biochar and biochar-based fertilizers enhance soil bacterial communities, which in turn improve crop yield and product quality. This study highlights the potential of biochar-based fertilizers as a sustainable agricultural practice to enhance soil health and crop quality through microbial community modulation.