The rational engineering of molecules is a powerful chemistry tool of pivotal importance in the fields of molecular magnetism and luminescence. Hence, systems that can be modulated via molecular engineering and composition control are expected to present extra versatility regarding the tunability of their properties. This is the case with molecular cluster aggregates (MCAs), high nuclearity molecular compounds. Herein, we demonstrate how the union of both strategies, namely, composition control and molecular engineering, can be employed to enhance molecular upconversion in MCAs. This was achieved by doping a {Gd8Er2Yb10} MCA with CeIII ions. By replacement of the optically silent GdIII ions with CeIII, the upconversion mechanism is modified due to CeIII-mediated cross-relaxation. In addition to this effect, we could also engineer the degree of metal site distortion due to the larger size of CeIII ions, relaxing the selection rules and impacting the upconversion quantum yield and luminescent thermometry. Opto-structural correlations demonstrate that the presented molecular engineering strategy can be used to enhance the performance of molecular upconverters.