The selective functionalization of the inner and outer surfaces of colloidal mesoporous silica (CMS) nanoparticles with different trialkoxysilanes, following a newly developed delayed co-condensation approach, results in bifunctional CMS. Complementary CMS nanoparticles were prepared with two different functional groups located either on the outer shell or in the inner core of the particle. The identification and localization of the functional groups was achieved by means of different techniques including zeta potential, nitrogen sorption measurements, and fluorescence spectroscopy. This last technique was applied to fluorescein isothiocyanate (FITC)-labeled CMS featuring aminopropyl functional groups on the periphery or the internal pore surface of the particles. Fluorescence quenching experiments were carried out with dodecanethiolate-stabilized gold nanoparticles having a diameter greater than the pore size of the CMS. It could be shown that fluorescence quenching occurs only when the FITC is positioned on the outer surface of the CMS nanoparticles, whereas no quenching was observed for FITC located in the inner core of the nanoparticle. These results clearly confirm the controlled localization of the aminopropyl groups in the nanometer space of the CMS particles. Our approach thus offers the opportunity to synthesize, in a novel multistep co-condensation strategy, various bifunctional mesoporous nanoparticles with controlled localization of different functional groups in the inner core or on the outer shell of the nanoparticle.