Biological fate and toxicity of nanoparticles (NPs) are connected to the interaction between NPs and the protein corona (PC) spontaneously forming around NPs in biological matrixes. PC is a dynamic entity that confers biological identity to NPs. In this work, fluorescence cross-correlation spectroscopy (FCCS) is used to study the impact of specific interactions between the NP surface and proteins on the intracellular fate of PC. The stability of the PC formed around glucosamide-functionalized Au-NPs from ConcanavalinA (ConA) or Bovine Serum Albumin (BSA) is characterized by FCCS. The NPs show higher affinity for ConA and competitive assays show that ConA easily exchanges BSA. A549 cells are exposed to glucosamide-functionalized Au-NPs with preformed ConA and BSA PCs. Intracellularly the frequency of cross-correlation for Au NPs with ConA PC remains constant to a 70% value until 24 h while for BSA it decreases to a 15% during the same period. FCCS measurements in several locations in the cell point out a different level of aggregation for the NPs with either ConA or BSA PCs. Our results show that the affinity of NPs functionalized with a ligand with affinity for a specific protein in bulk is retained intracellularly influencing NP fate and translocation.