The purpose of the study is to unravel the effects of inorganic Nitrogen (N) combined with either organic fertilizer or biochar on the soil biochemical properties, plant phenotypic characteristics and soil bacterial community structure within an experimental cotton field. The experiment involved the determination of the soil chemical properties, enzymatic activities and bacterial community. The study method employed field measurements, laboratory analyses, high throughput sequencing of the bacterial 16S rDNA to examine the response of soil enzymatic activities, microbial communities and plant phenotypic properties to the applied three different fertilizer regimens; (1) inorganic fertilizer (N), (2) N + organic fertilizer (N + OF), (3) N + biochar fertilizer (N + Biochar), under two cotton varieties: CN01 and ZD2040. The study indicated that combined N plus carbon-based organic fertilizer is responsible for enhanced crop growth, yield productivity and probiotic soil microbial content. Further, the combined mineral and carbon-based fertilizer regimen is highly beneficial to soil microbial content and diversity. The occurrence could be due to the increased soil nutrient content as a result of availability of carbon-based fertilizer and induced microbial activity by the mineral fertilizer. The use of N plus carbon-based organic fertilizer is recommended to improve the soil quality and cotton yield.