Cacao (Theobroma cacao) is significantly impacted each year by Frosty Pod Rot (FPR) caused by Moniliophthora roreri and Black Pod Rot (BPR) caused by Phytophthora species. The losses from these diseases pose a severe threat to cacao production worldwide. Consequently, cacao breeding programs focus on developing new clones that demonstrate high productivity potential and disease resistance. However, achieving this goal is challenging due to the lengthy selection process, the influence of environmental conditions on disease severity, and the need to avoid chemical control methods. Genetic resistance is, therefore, the most viable option for selecting and introducing new cacao clones to farmers. In this study, 40 cacao clones were evaluated from 2013 to 2017, with 20 clones sourced from the “Centro Agronómico Tropical de Investigación y Enseñanza” (CATIE) breeding program and 20 from the Fundación Hondureña de Investigación Agrícola (FHIA) breeding program. Three criteria were employed for clone selection: yield, percentage of diseased pods (PDP), and disease and production index (DPI). The results indicated that, depending on the objectives of the breeding program, these criteria can effectively be used to select new cacao clones that are both highly productive and disease-resistant. It was noted that cacao clones with high productivity are not always the most resistant to diseases, and vice versa. However, by combining these criteria, it is possible to identify cacao clones exhibiting high productivity potential and resistance to FPR and BPR.