The synthesis and characterization of amino‐functionalized mesoporous silica nanoparticles are presented following two different synthetic methods: co‐condensation and post‐synthesis grafting of 3‐aminopropyltriethoxysilane. The amino groups’ distribution on the mesoporous silica nanoparticles was evaluated considering the aggregation state of a grafted photosensitizer (Verteporfin) by using spectroscopic techniques. The homogeneous distribution of amino groups within the silica network is a key factor to avoid aggregation during further organic functionalization and to optimize the performance of functionalized silica nanoparticles in biomedical applications. In addition, the formation of a protein corona on the external surface of both bare and amino‐functionalized mesoporous silica was also investigated by adsorbing Bovine Serum Albumin (BSA) as a model protein. The adsorption of BSA was found to be favorable, reducing the aggregation phenomena for both bare and amino‐modified nanoparticles. Nevertheless, the dispersant effect of BSA was much more evident in the case of amino‐modified nanoparticles, which reached monodispersion after adsorption of the protein, thus suggesting that amino‐modified nanoparticles can benefit from protein corona formation for preventing severe aggregation in biological media.