Cocoa productivity is constrained by several challenges, including aging cocoa trees, limited availability of improved planting materials, pest and disease infestations, and the effects of climate change. The genetic diversity present among cocoa clones is therefore essential for developing superior hybrid cultivars that can address these issues and contribute to sustainable production. This study assessed the genetic diversity of forty cocoa clones established in an existing germplasm plot at the Cocoa Research Institute of Nigeria (CRIN), Ibadan, using a randomized complete block design with six replications. Seven quantitative pod traits were evaluated and analyzed statistically. Significant differences (P < 0.001) were observed among the forty clones for all traits measured. The clones exhibited wide variation in pod weight (203.33–837.67 g), number of beans per pod (33.67–56.67), bean weight per pod (52.50–174.00 g), pod length (12.17–27.70 cm), pod width (6.07–9.00 cm), pod thickness (0.5–1.87 cm), and hundred dry bean weight (58.00–154.00 g). Yield-related traits showed strong positive correlations with one another (P < 0.001). The first three principal component axes accounted for 76.2% of the total variation, and cluster analysis grouped the clones into five distinct categories. High phenotypic and genotypic coefficients of variation, along with high heritability and genetic advance, were recorded for pod weight, bean weight per pod, and hundred dry bean weight, while number of beans per pod and pod length exhibited high heritability with moderate genetic advance. These traits can therefore serve as key selection criteria in cocoa breeding programs.