Squaraine dyes, that exhibit intense absorption in the red/near infrared region, have been successfully introduced into mesoporous silica nanoparticles (MSNs) to obtain a nanoplatform for photodynamic therapy. Three brominated squaraine dyes which exhibited good PS performance in solution but a different behaviour in vitro due to cell permeability issues were used as photosensitizers. The effects of the adsorption within the pores of MSNs on the overall UV-Vis-NIR absorption and emission properties as well as on the PS performance was evaluated via a combined experimental and computational physico-chemical approach, which allowed us to correlate the unusual optical properties of two out of three systems with the dimerization of squaraines on the silica surface, with detrimental effects on the PS performance. Conversely, the nanoplatform where the squaraine molecules are adsorbed as monomers on the silica surface exhibited the best activity in singlet oxygen generation.