Wild maize (teosinte) has been reported to be less susceptible to biotic and abiotic stresses than its modern relative, corn. The composition of the teosinte root microbiome may be linked to traits such as drought tolerance and pest resistance. Trichoderma spp. are ubiquitous saprotrophic fungi found in the plant rhizosphere, enhancing host plant growth and crop productivity while alleviating biotic and abiotic stresses. The present study identified ten Trichoderma fungal isolates associated with the rhizosphere microbiome of teosinte (Zea mays spp. mexicana) and performed in vitro screening to assess both their multi-trait plant growth-promoting activities and their biological control potential against the phytopathogens Aspergillus flavus and Fusarium verticillioides. Additionally, interaction tests were conducted to evaluate the phytostimulant effect of Trichoderma spp. on maize (Zea mays) seed germination. Taxonomic and phylogenetic analysis identified five different Trichoderma species: T. rifaii (TA and TH); T. azevedoi (TB and TI); T. afroharzianum (TE); T. hamatum (TF and TG); and Trichoderma sp. (aff. bannaense) (TC, TD, and TJ). Partial least squares discriminant analysis revealed the isolates TF, TG, and TJ to have the highest potential for use as biocontrol and biostimulant agents. The present study is the first to examine Trichoderma species associated with the teosinte microbiome, and the results suggest that Trichoderma isolates are a potential sustainable alternative for improving maize cultivation.