The similarities and differences between foods produced under organic (OP) and conventional (CP) systems remain a controversial topic. In order to contribute to the evolution of this theme, grapes and juices were produced from vineyards in OP (n = 20) and CP (n = 20). All juices were elaborated using the same processing technology. Grape productivity was evaluated, and the classic characterization of juices was performed, followed by an in-depth characterization of mineral composition, pesticide residues, volatile compounds, phenolic compounds, and anthocyanins, as well as sensory analysis. In total, 101 dependent variables were monitored. From this set of variables, it was observed that grape productivity and the overall classic composition of juices from OP and CP systems are equivalent. Similarly, the mineral composition was equivalent, exception of the presence of a high concentration of Al in only one juice from the CP. As expected, pesticide occurrence was more frequent in CP juices (14/20), however, in all cases at much lower levels (1600 times lower or more) than the limits allowed by regulations. Residue occurrence also occurred in OP juices (2/20), which are not allowed by current regulations. In terms of volatile compounds profiles, 40 compounds were identified and quantified in OP juices, and 34 in CP juices. Regarding total phenolic compounds and total anthocyanins, the juices were equivalent. OP juices had a higher sensory preference. In conclusion, among101 variables evaluated, 75 indicate that the juices are equivalent. The 26 variables leading to technical differences are related to: 1) a higher frequency of residues in CP juices compared to OP juices; 2) a greater diversity of volatile compounds in OP juices; 3) differences in minor phenolic compounds and anthocyanins; and, 4) preference for OP juices.