Headspace analysis of highly humid samples remains a challenge for artificial olfaction. Based on surface plasmon resonance imaging and bio-based sensors, the NeOse Pro olfactive analyzer yields multivariate data and enhances the statistical discrimination capacity of odor patterns. However, the presence of a high background signal, such as water vapor from aqueous samples, may deteriorate its discriminant ability. Recently, miniaturized pre-concentrators packed with hydrophobic adsorbent have been developed to improve the detection limit of gas analysis methods and to enhance their selectivity by reducing the water’s background signal. This work presents, for the first time, the coupling of a miniaturized silicon micro pre-concentration unit (µPC) to a bio-based opto-electronic nose (NeOse Pro). The results showed that the coupling of a silicon µPC with the NeOse Pro led to an improvement in the detection limit of n-nonane by at least a factor of 125. Additionally, principal component analysis (PCA) of eight different flavored waters showed an enhanced discrimination ability of the coupled set-up in highly humid conditions.