The origin of organization of nanostructured silica coatings deposited on stainless steel substrates by remote microplasma at atmospheric pressure is investigated. We show by resorting to thermal camera measurements coupled with modelling that deposition, limited to a few seconds in time, occurs at low temperature (~below 420 K) although the gas temperature may reach 1400 K. Raman analyses of deposited films with thicknesses below 1 µm show the presence of oxidized silicon bonded to the metallic surface. The origin of nanodots is explained as follows. Close to the microplasma nozzle, the concentration of oxidizing species and/or the temperature being high enough, a silica thin film is obtained, leading to ceramic-metallic oxide interface that leads to a Volmer-Weber growth mode and to the synthesis of 3D structures over long treatment times. Far from the nozzle, the reactivity decreasing, thin films get a plasma-polymer like behaviour which leads to a Franck-Van der Merwe growth mode and films with a higher density. Other nanostructures, made of hexagonal cells, are observed but remain unexplained.