Among the different synthesis approaches to colloidal nanocrystals a recently developed toolkit is represented by cation exchange reactions, where the use of template nanocrystals gives access to materials that would be hardly attainable via direct synthesis. Besides, post-synthetic treatments, such as thermally activated solid state reactions, represent a further flourishing route to promote finely controlled cation exchange. Here, we report that, upon in situ heating in a transmission electron microscope, Cu2Se nanocrystals deposited on an amorphous solid substrate undergo partial loss of Cu atoms, which are then engaged in local cation exchange reactions with Cu “acceptors” phases represented by rod- and wire- shaped CdSe nanocrystals. This thermal treatment slowly transforms the initial CdSe nanocrystals into Cu2-xSe nanocrystals, through the complete sublimation of Cd and the partial sublimation of Se atoms. Both Cu “donor” and “acceptor” particles were not always in direct contact with each other, hence the gradual transfer of Cu species from Cu2Se or metallic Cu to CdSe nanocrystals was mediated by the substrate and depended on the distance between the donor and acceptor nanostructures. Differently from what happens in the comparably faster cation exchange reactions performed in liquid solution, this study shows that slow cation exchange reactions can be performed at the solid state, and helps to shed light on the intermediate steps involved in such reactions.