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The work analyzed the effect of two types of low-input farming conditions on the yield components and on the bioactive compounds in the pulp and peel of tomato fruits. The first low-input (LI) system involved the application of cow manure and manual weed control; in the second (LI^MI), the same system was integrated with mulching (the wood chips of eucalyptus) and intercropping (basil and cabbage plants). The study included the line 392, harboring the <i>hp-2</i> gene that increases the pigments of plant and fruit; the line 446 with the <i>atv</i> and <i>Aft</i> genes which influence the content of polyphenols; and a commercial control (cv. Rio Grande). The experimental design was a split-plot where the farming system (LI and LI^MI) was allocated in the main plot and the genotype was in the sub-plot. Within the main plot, each genotype was replicated three times in three randomized blocks. Mulching and intercropping led to a differentiation in the LI^MI with respect to the LI system with higher values of the leaf greenness index (61.3 vs. 53.3 Spad units), the number of fruits (70 vs. 46), and the weight of fruits per plant (2716.6 vs. 2195.0 g). However, the LI system showed a higher content of polyphenols (+37.9%) and anthocyanins (+116.7%) in the peel and a higher content of vitamin C (+44.0%) and polyphenols (+11.1) in the pulp. The less complex LI system stimulated the plants to produce natural antioxidant systems to contrast biotic and abiotic offenders, while the introduction of mitigation elements in the LI^MI system reduced the need for protective barriers against the environmental stress. The study also revealed that low-input systems can allow for satisfactory yields, minimizing the use of off-farm resources. Growers can combine factors of sustainable agriculture with specific genotypes to maximize the production of healthier foods.