This paper presents a unique perspective on enhancing the physicochemical mechanisms of two distinct highly sensitive nanostructured metal oxide micro hot plate gas sensors by utilizing an innovative multifrequency interrogation method. The two types of sensors evaluated here employ an identical silicon transducer geometry but with a different morphological structure of the sensitive film. While the first sensing film consists of self-ordered tungsten oxide nanodots, limiting the response kinetics of the sensor-chemical species pair only to the reaction phenomena occurring at the sensitive film surface, the second modality is a three-dimensional array of tungsten oxide nanotubes, which in turn involves both the diffusion and adsorption of the gas during its reaction kinetics with the sensitive film itself. By utilizing the proposed multifrequency interrogation methodology, we demonstrate that the optimal temperature modulation frequencies employed for the nanotubes-based sensors to selectively detect hydrogen, carbon monoxide, ethanol, and dimethyl methyl phosphonate (DMMP) are significantly higher than those utilized for the nanodot-based sensors. This finding helps understand better the amelioration in selectivity that temperature modulation of metal oxides brings about, and, most importantly, it sets the grounds for the nanoengineering of gas-sensitive films to better exploit their practical usage.