Squalene based nanoparticles obtained via nanoprecipitation are promising candidates as efficient anti-cancer drugs. In order to highlight their preparation process and to facilitate further clinical translation, the present study enlightens the paramount role of the solvent in the formation of these nanomedicines. Three different squalene-based nanoparticles, i.e. squalenic acid, deoxycytidine squalene and gemcitabine squalene, have been investigated before and after organic solvent evaporation. Size and structural analysis by Small Angle Neutron Scattering revealed that droplets' size was uniquely controlled by the solvent composition (ethanol-water), which evolved during their gradual formation. The particles were preferably swollen by water and the swelling increased when less ethanol was present. Either coalescence or fragmentation was observed depending on the increase or decrease of the ethanol content, supporting an equilibrium control of the size. Moreover, a high water swelling was observed for the three local organization of the nanodroplets (hexagonal for gemcitabine squalene, cubic for deoxycytidine and not structured for squalenic acid) and could be the source of the previously reported efficiency of related anti-cancer squalene based nanomedicines.