Biomolecules in bodily fluids such as plasma can adsorb to the surface of nanoparticles and influence their biological properties. This phenomenon, known as the protein corona, is well established in the field of synthetic nanotechnology but has not been described in the context of plant virus nanoparticles (VNPs). We investigated the interaction between VNPs derived from Tobacco mosaic virus (TMV) and plasma proteins, and found that the VNP protein corona was significantly less abundant compared to the corona of synthetic particles. The formed corona was dominated by complement proteins and immunoglobulins, the binding of which could be reduced by PEGylating the VNP surface. We investigated the impact of the VNP protein corona on molecular recognition and cell targeting in the context of cancer and thrombosis. A library of functionalized TMV rods with PEG and peptide ligands targeting integrins or fibrin(ogen) showed different dispersion properties, cellular interactions and in vivo fates depending on the properties of the protein corona, influencing target specificity and non-specific scavenging by macrophages. Our results provide insight into the in vivo properties of VNPs and suggest that the protein corona effect should be considered during the development of efficacious, targeted VNP formulations.