Preclinical studies of nanoparticles for pulmonary therapeutics are often performed on 2D cell cultures or in vitro models that do not include a mucus barrier. However, the mucus layer lining the lungs is an essential barrier for drugs to permeate in order to exert a therapeutic effect. Herein, the role of surface coating of lanthanide‐doped upconverting nanoparticles (UCNPs) and their interaction with the mucus barrier are explored using a patient‐derived 3D cell culture model. The upconverted emissions from the UCNPs are used to track them throughout the 3D model and study their localization as a function of administration time and mucus thickness. Positively charged, ligand‐free, and negatively charged, supported lipid bilayer‐coated UCNPs are evaluated. A substantial difference in the residence time in mucus and mucociliary clearance of each type of UCNP is observed in a realistic and relevant model. As such, these results underscore the need for preclinical investigations in tissue models, especially with respect to the surface properties of the nanoparticles under study.