The consumption of natural foods is increasingly high, and in recent years, consumers have preferred foods from systems with responsible management of natural resources (organic, hydroponic). However, there are still contradictions regarding the nutritional content of products from these different types of crops. Our study aims to compare, for the first time, the content of antioxidants (ascorbic acid, lycopene, total phenolics, essential fatty acids), micronutrients (copper, iron, manganese, zinc), contaminants (cadmium and lead), and free radical scavenging activity between conventional, organic, and hydroponic tomatoes (Solanum lycopersicum) sold in markets in Quito, Ecuador. Ascorbic acid and lycopene were determined by HPLC/UV-Vis. Total phenolics (Folin–Ciocalteu method) and free-radical scavenging activity (2,2-diphenyl-1-picrylhydrazyl method) were determined via UV-Vis spectrophotometry. Lipid profiles were determined as fatty acid methyl esters through a GC-FID. Trace metals were determined using FAAS (micronutrients), and GFAAS (pollutants). No significant differences (p > 0.05) between antioxidant and micronutrient content among the three types of tomatoes were found. Regarding cadmium and lead, the contents were below the Codex Alimentarius threshold limits. Finally, free radical scavenging activity varied slightly (organic > hydroponic > conventional). Although the samples showed certain differences in antioxidant content, none of the tomato types could be considered nutritionally better because of the high variability of the results.