Assessment of the genetic diversity within existing germplasm is essential for the sustainable management of plant genetic resources, and the development of improved cultivars. Dioscorea alata is considered as one of the most widespread root and tuber crop species in tropical regions, and significantly contributes to enhancing the income of small-scale producers and improving food security. This study was conducted to profile the genetic variability within a panel of 205 D. alata accessions using 15 key yam tuber traits. Multivariate analysis revealed high variability among the accessions for the evaluated traits. Based on the clustering methods, the accessions were grouped into four main clusters with different genetic performance. Furthermore, silhouette (Si) analysis indicated that tuber quality-related traits clustered the accessions more distinctly than tuber quantitative traits, with the highest coefficient of 0.58. A subset of traits, including flesh color, flesh oxidation, and tuber shape, emerged as the most relevant variables for cluster differentiation based on tuber quality. Meanwhile, yield, circumference, and length were the key quantitative traits that best defined the clusters. Among the relevant variables identified by PLS-DA, only tuber circumference and tuber length significantly predicted tuber yield, with regression coefficients of 0.55 and 0.35, respectively. Tuber browning was the trait that reduced cooking quality, and multi-trait genotype–ideotype distance index (MGIDI) analysis identified genotypes performing better within each cluster defined by tuber quantitative traits for water yam breeding programs. This study provides reliable and valuable insights into the genetic variability within Côte d'Ivoire's water yam germplasm and consitutes a reliable source for genetic improvement.