Abstract Soil fertility and productivity are severely impacted by exploitation and degradation processes. These threats, coupled with population growth and climatic changes, compel us to search for innovative agroecological solutions. Prebiotics, a type of soil biostimulant, are used to enhance soil conditions and plant growth and may play a role in carbon (C) sequestration. Two commercial prebiotics, K1® and NUTRIGEO L® (referred to as SPK and SPN, respectively), were assessed for their effects on agricultural soil cultivated with Zea mays L., compared to untreated soil or control (SP). Analyses were performed at two harvesting dates: three weeks (D1) and ten weeks (D2) after the application of prebiotics. Plant growth parameters and soil characteristics were measured, focusing on soil organic matter, soil bacterial and fungal communities, and plant root mycorrhization. Regarding physicochemical parameters, both prebiotic treatments increased soil electrical conductivity, cation exchange capacity, and soluble phosphorus (P) while decreasing nitrates. Meanwhile, the SPN treatment was distinct in elevating specific cationic minerals, such as calcium (Ca) and boron (B), at D2. At the microbial level, each prebiotic induced a unique shift in the indigenous bacterial and fungal communities’ abundance and diversity, evident at D2. Simultaneously, specific microbial taxa were recruited by each prebiotic treatment, such as Caulobacter , Sphingobium , and Massilia from bacteria and Mortierella globalpina and Schizothecium carpinicola from fungi in SPK as well as Chitinophaga , Neobacillus , and Rhizomicrobium from bacteria and Sordariomycetes and Mortierella minutissima from fungi in SPN. These biomarkers were identified as (a) saprotrophs, (b) plant growth-promoting bacteria and fungi, (c) endohyphal bacteria, and (d) endophytic and symbiotic microbiota. This result was reflected in the increase in glomalin content and mycorrhization rate in the treated soils, especially by SPN. We observed that these effects led to an increase in plant biomass (shoots by 19% and 22.8% and roots by 47.8% and 35.7% dry weights for SPK and SPN, respectively) and contributed to an increase in soil C content (organic C by 8.4% and total C by 8.9%), particularly with SPN treatment. In light of these findings, the use of prebiotics ten weeks after application not only increased plant growth by improving soil characteristics and shaping its native microbial community but also demonstrated the potential to enhance C sequestration.