The fabrication of uniform and patterned nanocrystal (NC) assemblies has been investigated by exploiting the possibility of carefully tailoring colloidal NC surface chemistry and the ability of polyelectrolyte (PE) to functionalize substrates through an electrostatic layer-by-layer (LbL) strategy. Appropriate deposition conditions, substrate functionalization, and post-preparative treatments were selected to tailor the substrate surface chemistry to effectively direct the homogeneous electrostatic-induced assembly of NCs. Water-dispersible luminescent NCs, namely, (CdSe)ZnS and CdS, were differently functionalized by (1) ligand-exchange reaction, (2) growth of a hydrophilic silica shell, and (3) formation of a hydrophilic inclusion complex, thus providing functional NCs stable in a defined pH range. The electrostatically charged functional NCs represent a comprehensive selection of examples of surface-functionalized NCs, which enables the systematic investigation of experimental parameters in NC assembly processes carried out by combining LbL procedures with microcontact printing and also exploiting NC emission, relevant for potential applications, as a prompt and effective probe for evaluating assembly quality. Thus, an ample showcase of combinations has been investigated, and the spectroscopic and morphological features of the resulting NC-based structures have been discussed.