Frosty pod rot, caused by the fungus Moniliophthora roreri, is one of the most important diseases of cacao in Peru. Sustainable alternatives to control it include timely cultural practices such as pruning, and the application of biological control agents such as Trichoderma spp. We isolated 234 Trichoderma strains native to the department of Amazonas in Northern Peru from soil samples in cacao farms. These strains belong to at least eighteen species within four phylogenetic clades in the genus (Harzianum, Longibrachiatum, Hamatum, and Brevicompactum clades). We aimed to assess the in vitro biocontrol potential of these strains against M. roreri. We evaluated their mycoparasitism, antibiosis, and potential antagonism to select candidate strains for efficient biocontrol of M. roreri. We found evidence (Kruskal–Wallis test, p < 0.005) that strains belonging to the Harzianum clade tend to have higher mycoparasitism, antibiosis, and potential antagonism levels than strains in the Longibrachiatum and Hamatum clades. Additionally, this study constitutes the first report for antagonistic behavior against M. roreri for T. parareesei, T. lentiforme, T. orientale, T. asperelloides, T. inhamatum, T. zelobreve, T. afarasin, T. ghanense, T. rifaii, and T. breve. These results will be foundational for further M. roreri biocontrol studies.