We discuss the construction of a nuclear Energy Density Functional (EDF) from ab initio calculations, and we advocate the need of a methodical approach that is free from ad hoc assumptions. The equations of state (EoS) of symmetric nuclear and pure neutron matter are computed using the chiral NNLO$_{rm sat}$ and the phenomenological AV4$^prime$+UIX$_{c}$ Hamiltonians as inputs in the Self-consistent Greens Function (SCGF) and Auxiliary Field Diffusion Monte Carlo (AFDMC) methods, respectively. We propose a convenient parametrization of the EoS as a function of the Fermi momentum and fit it on the SCGF and AFDMC calculations. We apply the ab initio-based EDF to carry out an analysis of the binding energies and charge radii of different nuclei in the local density approximation. The NNLO$_{rm sat}$-based EDF produces encouraging results, whereas the AV4$^prime$+UIX$_{c}$-based one is farther from experiment. Possible explanations of these different behaviors are suggested, and the importance of gradient and spin-orbit terms is analyzed. Our work paves the way for a practical and systematic way to merge ab initio nuclear theory and DFT, while at the same time it sheds light on some of the critical aspects of this procedure.