Ordered mesoporous silica materials have been proposed as promising drug delivery systems and bone tissue regeneration precursors. In the present work, the behavior of colloidal mesoporous silica (CMS) nanoparticles was investigated in simulated biological fluid with the aim of gaining new insights about the reactivity of the CMS when brought into contact with biological media that simulate the human plasma, in view of drug delivery applications. The effect of surface functionalization on the stability of the CMS was also examined. Unfunctionalized, phenyl-, chloropropyl- and aminopropyl-functionalized and poly(ethylene glycol)-coated CMS nanoparticles were studied. The samples were prepared by a co-condensation approach and brought into contact with Simulated Body Fluid (SBF) at 37 °C for 1 month. The results at defined time intervals show a partial degradation of the unfunctionalized and of the three organo-functionalized CMS, which takes place, depending on the surface functionalization, between the first 2 and 24 h of immersion in SBF. After 1 month, the textural properties of the mesoporous systems were lost and pore blocking occurred simultaneously with the precipitation of inorganic compounds from the SBF solution. In particular, the presence of hydroxyapatite (HAp) was detected on the CMS particles. The attachment of a poly(ethylene glycol)-layer on the outer surface of CMS stabilizes the CMS by reducing the rate of degradation within the first days of immersion in SBF. Thus the surface-coating with PEG offers the possibility to enhance the bio-stability of functionalized CMS nanoparticles, which is of great interest for future injectable blood-persistent biomedical systems and site-specific drug delivery devices.