Thermoresponsive microgels are one of the most investigated class of soft colloids, thanks to their ability to undergo a Volume Phase Transition (VPT) close to ambient temperature. However, this fundamental phenomenon still lacks a detailed microscopic understanding, particularly regarding the presence and the role of charges in the deswelling process. Here we fill this gap by combining experiments and simulations to show that the microgel collapse does not happen in a homogeneous fashion, but through a two-step mechanism, entirely attributable to electrostatic effects. The signature of this phenomenon is the emergence of a minimum in the ratio between gyration and hydrodynamic radii at the VPT. Thanks to simulations of several microgels with different cross-linker concentrations, charge contents and charge distributions, we build a unifying master-curve able to predict the two-step deswelling. Our results have direct relevance on fundamental soft condensed matter science and on microgel applications ranging from materials to biomedical technologies.