It is known that poorly performed fertigation directly impacts on tomato production and biometric components. In addition, consumers are also affected by interrelated characteristics that interfere with the acceptability of the fruit, such as the physicochemical parameters and nutrients in the fruit. Thus, eco-friendly technologies, such as irrigation with ultra-low frequency electromagnetic treated-water, which attenuates the inadequate management of fertigation, are essential to improve marketable fruit yields. Thus, the objective of the present work was to investigate the impact of treated water with very low-frequency electromagnetic resonance fields in physical, chemical and nutritional parameters at different nutrient solution strengths in tomato fruits. In this study, experiments were carried out in randomized blocks and five doses of fertigation were used (1.5; 2.5; 4.0; 5.5; and 7.0 dS m−1), employing two types of water: electromagnetically treated and untreated. It can be seen that the fertigation affected some parameters, mainly the number of fruits with blossom-end rot, fruit size, and weight. Variance analysis (ANOVA) was performed with the subsequent use of the Tukey test. In all statistical tests, a confidence level of 95% was considered. The soluble solids content increased by 28% as a function of the fertigation doses. The electromagnetically treated water reduced the number of fruits with blossom-end rot by 35% (p < 0.05). Overall, electromagnetic water improved the physicochemical quality parameters and the nutritional status of tomato fruits. Thus, this study demonstrated that green technology could leverage tomato fruit production and quality.