Two major improvements to the state-of-the-art Repeating Electrostatic Potential Extracted Atomic (REPEAT) method, for generating accurate partial charges for molecular simulations of periodic structures, are here developed. The first, D-REPEAT, consists in the simultaneous fit of the electrostatic potential (ESP), together with the total dipole fluctuations (TDF) of the framework. The second, M-REPEAT, allows the fit of multiple ESP configurations at once. When both techniques are fused into one, DM-REPEAT method, the resulting charges become remarkably stable over a large set of fitting regions, giving a robust and physically sound solution to the buried atoms problem. The method capabilities are extensively studied in ZIF-8 framework, and subsequently applied to IRMOF-1 and ITQ-29 crystal structures. To our knowledge, this is the first time that this approach is proposed in the context of periodic systems.