QTL and candidate genes associated to fruit quality traits have been identified in a tomato genetic map derived from Solanum pimpinellifolium L., providing molecular tools for marker-assisted breeding. The study of genetic, physiological, and molecular pathways involved in fruit development and ripening has considered tomato as the model fleshy-fruited species par excellence. Fruit quality traits regarding organoleptic and nutritional properties are major goals for tomato breeding programs since they largely decide the acceptance of tomato in both fresh and processing markets. Here we report the genetic mapping of single-locus and epistatic quantitative trait loci (QTL) associated to the fruit size and content of sugars, acids, vitamins, and carotenoids from the characterization of a RIL population derived from the wild-relative Solanum pimpinellifolium TO-937. A genetic map composed of 353 molecular markers including 13 genes regulating fruit and developmental traits was generated, which spanned 1007 cM with an average distance between markers of 2.8 cM. Genetic analyses indicated that fruit quality traits analyzed in this work exhibited transgressive segregation and that additive and epistatic effects are the major genetic basis of fruit quality traits. Moreover, most mapped QTL showed environment interaction effects. FrW7.1 fruit size QTL co-localized with QTL involved in soluble solid, vitamin C, and glucose contents, dry weight/fresh weight, and most importantly with the Sucrose Phosphate Synthase gene, suggesting that polymorphisms in this gene could influence genetic variation in several fruit quality traits. In addition, 1-deoxy-D-xylulose 5-phosphate synthase and Tocopherol cyclase genes were identified as candidate genes underlying QTL variation in beta-carotene and vitamin C. Together, our results provide useful genetic and molecular information regarding fruit quality and new chances for tomato breeding by implementing marker-assisted selection.