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Functionalized titanium dioxide (TiO2) nanoparticles (NPs) with intense fluorescent dyes are a promising tool for several technological applications ranging from photochemistry, photocatalysis, photovoltaics, photodynamic therapy, or bioimaging. Here, we present the case study of Alizarin adsorption on TiO2 NPs of different shapes and increasing size up to 2.2 nm (700 atoms), by means of density functional theory calculations. We find that Alizarin can bind in three different ways, depending on the number and the type of bonds between Alizarin and TiO2: ‘tridented’, ‘bidented’, and ‘chelated’. Next, we investigate the optical properties of these systems by time-dependent density functional theory calculations. Based on the absorption spectra and the Kohn–Sham orbitals analysis, we discovered that the mechanism of electron injection depends on the Alizarin binding mode to the TiO2 surface. While for bidented and chelated adsorption modes, a direct charge transfer is observed; for the tridented one, an indirect mechanism governs the charge transfer process following the excitation. Our results are in good agreement with existing experimental data and suggest that by tailoring the shape of the TiO2 NPs and, thus, determining the type of undercoordinated Ti atoms prevalently exposed at the surface, it is possible to control the predominant injection mechanism.