Aqueous solutions are the basis for most, biomedical assays, but they quench the upconversion luminescence significantly. Surface modifications of upconverting nanoparticles are vital for shielding the obtained luminescence. Modifications also provide new possibilities for further use by introducing attaching sites for biomolecule conjugation. We demonstrate the use of a layer-by-layer surface modification method combining varying lengths of negatively charged polyelectrolytes with positive neodymium ions in coating the upconverting NaYF4:Yb3+,Er3+ nanoparticles. We confirmed the formation of the bilayers and investigated the surface properties with Fourier transform infrared and reflectance spectroscopy, thermal analysis, and (zeta-potential measurements. The effect of the coating on the upconversion luminescence properties was characterized, and the bilayers with the highest improvement in emission intensity were identified. In addition, studies for the nanoparticle and surface stability were carried out in aqueous environments. It was observed that the bilayers were able to shield the materials' luminescence from quenching also in the presence of phosphate buffer that is currently considered the most disruptive environment for the nanoparticles.