The agromorphological traits and phenotypic variation of mineral content in the fruit were evaluated in eleven tomato accessions from nine communities in El Salvador. The tomato collection was cultivated in a greenhouse with a randomized complete block design with three replications. Plant phenological and fruit traits, as well as the mineral content, were evaluated using atomic-absorption and ultraviolet-visible spectroscopy. In the analysis of variance, significant differences (p < 0.01) among the accessions were determined for agromorphological traits and all mineral elements except Cu. Plant height at 30, 60 and 90 days after transplant, days to flowering and maturating of the fruits, and the number and weight of fruits per plant were useful variables for describing the phenotypic divergences among the tomato accessions. In terms of mineral content, the differences among the accessions were based on Mg, P, S, Fe, Zn and Mn. The weights of the fruits per cluster and per plant and fruit weight presented negative correlations with Ca, Mg, Fe and P (r = −0.67 to −0.71, p < 0.05) and a positive correlation with Na (0.63).