Upconverting nanoparticles (UCNPs) are being extensively investigated for applications in bioimaging because of their ability to emit ultraviolet, visible, and near-infrared light. NaYF4 is one of the most suitable host matrices for producing high-intensity upconversion fluorescence; however, UCNPs based on NaYF4 are not chemically stable in aqueous media. To prevent dissolution, their surfaces should be modified. We studied the formation of protective phosphonate coatings made of ethylenediamine(tetramethylenephosphonic acid), alendronic acid, and poly(ethylene glycol)-neridronate on cubic NaYF4 nanoparticles and hexagonal Yb3+,Er3+-doped upconverting NaYF4 nanoparticles (β-UCNPs). The effects of synthesis temperature and ultrasonic agitation on the quality of the coatings were studied. The formation of the coatings was investigated by transmission electron microscopy, zeta-potential measurements, and infrared spectroscopy. The quality of the phosphonate coatings was examined with respect to preventing the dissolution of the NPs in phosphate-buffered saline (PBS). The dissolution tests were carried out under physiological conditions (37 °C and pH 7.4) for 3 days and were followed by measurements of the dissolved fluoride with an ion-selective electrode. We found that the protection of the phosphonate coatings can be significantly increased by synthesizing them at 80 °C. At the same time, the coatings obtained at this temperature suppressed the surface quenching of the upconversion fluorescence in β-UCNPs.