Prebiotics, a subset of biostimulants, have garnered attention for their potential to enhance soil conditions and promote plant growth, offering a promising alternative to conventional agricultural inputs. This study explores how two commercial prebiotics, K1® and NUTRIGEO L® (SPK and SPN), impact soil functions compared to a control (SP). The experiment involved agricultural soil amended with organic wheat straws and cultivated with Zea mays L. Previous research demonstrated substantial effects of these prebiotics on plant biomass, soil parameters, and microbial community ten weeks after application. The present study delves deeper, focusing on soil microbial abundance, enzyme activities, and metabolic diversity. Analysis revealed that SPN notably increased the fungi-to-bacteria ratio, and both prebiotics elevated the activity of several key enzymes. SPN enhanced α-glucosidase and β-galactosidase activities, while SPK increased arylsulfatase, phosphatase, alkaline phosphatase, and urease activities. Enzymatic indexes confirmed the positive impact on soil functional diversity and fertility. Additionally, prebiotic treatments showed distinct metabolic profiles, with SPK degrading eleven carbon sources more rapidly across five groups and SPN accelerating the decomposition rate of four carbon sources from three groups. These findings highlight the ability of prebiotics to shape microbial communities and enhance soil fertility by modulating their functional activity and diversity.