Different silica-protoporphyrin IX (PpIX) nanocomposites have been synthesized to evaluate the dependence of singlet oxygen production and bacterial inactivation efficiency on the morphology of the nanomaterials. Modulation of the synthetic procedure allowed obtaining silica nanoparticles with different porosity which were characterized by TEM and spectroscopic analysis after PpIX adsorption. Time-resolved phosphorescence measurements on the different nanoporous samples revealed that the porosity of the nanoparticles plays a pivotal role on the singlet oxygen production and release from the nanoparticles. Thus, apart from the expected decay of singlet oxygen outside the silica matrix, a second component has been observed for the porous materials, attributed to the decay of singlet oxygen inside the pores. The relative efficiency of singlet oxygen production resulted to be higher for the sample with the greatest pores volume. The capability of the nanocomposites to inactivate bacteria was tested in vitro on Staphylococcus aureus strain. Interestingly, the efficiency for singlet oxygen production of the nanocomposites and their bacterial inactivation efficiency followed a different trend, indicating that the relative position of the photosensitizer and the superficial properties of the particles affect the antibacterial activity of the overall system.