In biological fluids, nanoparticles (NPs) are in contact with proteins and other biomolecules. Proteins adsorb to NPs and form a coating called a protein corona (PC). The PC is known to greatly affect the interaction of NPs with biological systems. A comprehensive knowledge of the protein nanoparticle interaction is essential to understand the biological fate of NPs and for the design of NPs for biomedicine. Fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) are sensitive spectroscopy techniques that measure fluorescence intensity fluctuations of single molecules inside a femtoliter confocal volume. Both techniques are suitable for studying the formation of protein corona around NPs and for examining corona stability in situ in biological matrixes. In this review we provide a short description of FCS/FCCS and their application in PC studies, highlighting results from our work about the impact of surface chemistry of NPs on corona formation and NP intracellular fate.