Solanum muricatum Aiton, commonly known as sweet cucumber, is native to South America and had historical significance in pre-Incan civilizations such as the Moche, Nazca, and Wari. This study presents the morphological and preliminary phytochemical characterization of S. muricatum germplasm conserved at the Universidad Nacional de San Cristóbal de Huamanga (UNSCH), Peru. Two germplasm collection events were conducted. The first, in Ayacucho (Gutiérrez, 2023), yielded 24 accessions evaluated using a simple 5×5 lattice design with three replications, including Capsicum pubescens as an outgroup. Fifty qualitative and twenty-seven quantitative traits were assessed using IPGRI and COMAV descriptors. Cluster analysis identified four distinct groups, validating differentiation, with C. pubescens forming a separate clade. Grouping was also observed based on vegetative phenology, inflorescence, fruit, and seed traits. An ANOVA revealed highly significant differences among the accessions (p < 0.01) in agronomic traits such as the fruit count per inflorescence, fruit count per plant, and yield per plant. The second collection (Ramirez, 2024) included accessions from Cusco, Apurímac, Ayacucho, Ica, Lima, Cajamarca, and Lambayeque, contributing 35 accessions. Cluster analysis revealed seven distinct groups, and an ANOVA again showed significant variation (p < 0.01). The current ex situ germplasm bank now contains 59 asexually propagated accessions and 77 segregating lines grown from botanical seeds—126 genotypes in total. Phytochemical profiling of fruit peel from 12 morphologically representative accessions, alongside Physalis peruviana and Solanum betaceum controls, was conducted via HPLC using standards of caffeic acid, rosmarinic acid, cinnamic acid, quercetin, rutin, resveratrol, and chlorogenic acid. The results showed substantial variability in the total phenols (0.55–1.71 mg GAE/100 mg), antioxidant capacity (0.42–0.78 mg vitamin C/100 mg), flavonoids (0.13–0.24 mg quercetin/100 mg), hydroxycinnamic acids (0.25–1.11 mg caffeic acid/100 mg), carotenoids (6.62–33.02 mg/100 mg), and DPPH inhibition (IC₅₀: 103.23–1402.95 μg). Carotenoids and chlorogenic acid were the predominant compounds. These findings reveal significant genetic and phytochemical diversity within S. muricatum, supporting its potential for further biotechnological enhancement through genomics, transcriptomics, and metabolomics research at the UNSCH.