The efficacy of the very low frequency electromagnetic field in cancer treatment remains elusive due to a lack of explanatory mechanisms for its effect. We developed a novel thermodynamic model that calculates for every cell type the frequency capable of inhibiting proliferation. When this frequency was applied to two human cancer cell lines, it reduced their growth while not affecting healthy cells. The effect was abolished by the inhibition of calcium fluxes. We found evidences of an enhanced respiratory activity due to the increased expression of the elements of the respiratory chain and oxidative phosphorylation, both at the mRNA and protein level. The respiratory burst potentiated the production of reactive oxygen species but was not associated to increased levels of ATP, leading to the conclusion that the energy was readily spent in the adaptive response to the electromagnetic field. Taken together, our data demonstrate that, regardless of individual molecular defects, it is possible to control cancer cells with a specific irradiation that imposes a mitochondrial metabolic switch, regulating calcium fluxes and deleterious to cancer growth. This approach lays the foundations for a personalized cancer medicine.