In the kagome metals AV₃Sb₅ (A = K, Rb, Cs), three-dimensional charge order is the primary instability that sets the stage for other collective orders to emerge, including unidirectional stripe order, orbital flux order, electronic nematicity and superconductivity. Here, we use high-resolution angle-resolved photoemission spectroscopy to determine the microscopic structure of three-dimensional charge order in AV₃Sb₅ and its interplay with superconductivity. Our approach is based on identifying an unusual splitting of kagome bands induced by three-dimensional charge order, which provides a sensitive way to refine the spatial charge patterns in neighbouring kagome planes. We found a marked dependence of the three-dimensional charge order structure on composition and doping. The observed difference between CsV₃Sb₅ and the other compounds potentially underpins the double-dome superconductivity in CsV₃(Sb,Sn)₅ and the suppression of T_c in KV₃Sb₅ and RbV₃Sb₅. Our results provide fresh insights into the rich phase diagram of AV₃Sb₅.