Wild fruit species offer significant nutritional, environmental, and economic benefits. Among them, Prunus cerasifera Ehrh. (myrobalan) stands out for its resilience and nutrient-rich fruits, traditionally consumed fresh or dried. This study aimed to assess the morphological and biochemical diversity of 21 wild P. cerasifera accessions from Slovenia, focusing on 18 fruit and stone traits, including size, shape, color, and phenolic compounds such as total monomeric anthocyanins and total phenolic content (TPC). The objective was to identify genotypes with potential for cultivation and food production or as parental components in breeding programs. The results showed variability in fruit length (2.19–2.82 cm), width (2.18–2.99 cm), weight (67.98–150.30 g), firmness, and juiciness, with notable differences in stone characteristics. Phytochemical analysis revealed a wide range of TPC (277–1756 mg/100 g) and anthocyanin levels (0–710 mg/100 g), with higher concentrations in darker fruits. Statistical analysis compared PAM and AGNES clustering methods, finding that PAM with five clusters and AGNES with two clusters provided similar insights. The study emphasized variability in morphological and chemical traits among clusters, with specific accessions showing particularly valuable traits, such as accession RK13, which had high TPC and anthocyanins and a non-adherent stone.