Protective and ion selective polyelectrolyte multilayer coatings from poly(sodium 4-styrenesulfonate) and poly(diallyldimethylammonium chloride) were manufactured on the NaYF4:Yb3+,Er3+ upconverting nanoparticle surface. The ion selective coatings would be effective in hindering the disintegration of inorganic nanoparticle in an aqueous environment used in various applications such as in vitro assays and biomedical imaging. The disintegration is prominent especially in detrimental phosphate-based buffers. The effect of the used counteranion on the multilayer formation and the luminescent properties of the coated materials is discussed. The multilayer coating was confirmed with Fourier transform infrared spectroscopy, thermal analysis, and transmission electron microscopy. The behavior of the coated nanoparticles in aqueous environment was monitored by using fluoride ion selective electrode. We observed that the ion selective coatings prepared using fluoride or chloride as a counteranion were the most effective in slowing the disintegration of the nanoparticles. The deceleration in the disintegration process was observed also in phosphate-based buffer which emphasizes the ion selective properties of the multilayer coating. The upconversion luminescence measurements of the coated nanoparticles showed that coatings manufactured with bromide counteranion were most efficient in shielding the upconversion luminescence in solid state.