Soil fertility and productivity are severely impacted by exploitation and degradation processes. These threats, coupled with population growth and climatic changes, force us to search for innovative agroecological solutions. Prebiotics are one type of soil biostimulants that are used to enhance soil conditions, plant growth, and could contribute to improve carbon sequestration. In this context, our study was designed to evaluate and explain the effects of two commercial prebiotics (K1® and NUTRIGEO L®) on soil mixed with organic wheat straws and cultivated with Zea mays L. in comparison to untreated soil at two harvesting dates after their application (3 weeks D1 and 10 weeks D2). For that, we monitored plant growth criteria, soil physico-chemical parameters, soil organic matter (OM) evolution, and soil microbial community structure and diversity with emphases on indigenous microbial selection and root mycorrhization. The obtained results demonstrated the short- and medium-term positive effects of prebiotics on soil fertility and microbial community and their repercussions on plant biomass and carbon storage. Our aim is to confirm the vital role prebiotics will play as a new alternative approach in the agroecological transition toward modern, durable, and sustainable agriculture.