A general strategy to extend the interacting quantum atoms (IQA) approach to pseudopotential or effective core potential electronic Structure calculations is presented. With the protocol proposed here, the scope of IQA thinking opens to chemical bonding problems in heavy-atom systems, as well as to larger molecules than those presently allowed by computational limitations. We show that, provided that interatomic surfaces are computed from core-reconstructed densities, reasonable results are obtained by integrating reduced density matrices built from the pseudowave functions. Comparison with all-electron results in a few test systems shows that exchange-correlation energies are better reproduced than Coulombic contributions, an effect which is traced to inadequate atomic populations and leakage of the core population into the Surrounding quantum atoms.