Amorphous silica plays an important role in heterogeneous catalysis as a support and is frequently presumed to be “inert”. The structure of the supported catalyst is key to understanding the stability and reactivity of catalytic systems. To provide vital insights into the surface reactivity of silica, Polyhedral oligomeric silsesquioxanes (POSSs) can act as realistic homogeneous molecular models for silica surfaces. Here, we report novel reactivities associated with the silica surface, derived from our insights obtained by means of such model systems with potentially significant implications in catalysis when employing silica-supported catalysts. In this work, the gas-phase reactivities of two cyclohexyl-substituted POSSs, namely the completely condensed triganol prism [Si6cy6O9] (a6b0), and the incompletely-condensed partial cube [Si7cy7O9(OH)3] (a7b3), with cy=c-C6H11, were studied by using atmospheric pressure chemical ionisation (APCI) and collision-induced decomposition (CID) spectroscopies. Silsesquioxane a6b0, containing three-membered rings, was found to be much more reactive, undergoing novel CH2-insertion on reaction with gas phase molecules—a reaction not observed for a7b3, containing only four-membered rings. Both silsesquioxanes displayed the ability to trap ammonia formed in situ within the mass spectrometer from N2 in the instrument. This work also demonstrates the applicability of APCI and the role of CID in elucidating reactive POSS structures, highlighting novel gas-phase reactivities of POSS.