The interaction of (3-Aminopropyl)triethoxysilane (APTES) with pulsed late Ar-O-2 afterglow is characterized by the synthesis of OH, CO and CO2 in the gas phase as main by-products. Other minor species like CH, CN and C2H are also produced. We suggest that OH radicals are produced in a first step by dehydrogenation of APTES after interaction with oxygen atoms. In a second step, the molecule is oxidized by any O-2 state, to form peroxides that transform into by-products, break thus the precursor C-C bonds. If oxidation is limited, i.e. a low duty cycle, fragmentation of the precursor is limited and produced nanoparticles keep the backbone structure of the precursor, but contain amide groups produced from the amine groups initially available in APTES. At high duty cycle, silicon-containing fragments contain some carbon and react together and produce nanoparticles with a non-silica-like structure.