Certain biomarkers in exhaled breath are indicators of diseases in the human body. The non-invasive detection of such biomarkers in human breath increases the demand for simple and cost-effective gas sensors to replace state-of-the-art gas chromatography (GC) machines. The use of metal oxide (MOX) gas sensors based on thin-film structures solves the current limitations of breath detectors. However, the response at high humidity levels, i.e., in the case of exhaled human breath, significantly decreases the sensitivity of MOX sensors, making it difficult to detect small traces of biomarkers. We have introduced, in previous work, the concept of a hybrid gas sensor, in which thin-film-based MOX gas sensors are combined with an ultra-thin (20–30 nm) polymer top layer deposited by solvent-free initiated chemical vapor deposition (iCVD). The hydrophobic top layer enables sensor measurement in high-humidity conditions as well as the precise tuning of selectivity and sensitivity. In this paper, we present a way to increase the hydrogen (H₂) sensitivity of hybrid sensors through chemical modification of the polymer top layer. A poly(1,3,5,7-tetramethyl-tetravinylcyclotetrasiloxane) (PV4D4) thin film, already applied in one of our previous studies, is transformed into a silsesquioxane-containing top layer by a simple heating step. The transformation results in a significant increase in the gas response for H₂ ~709% at an operating temperature of 350 °C, which we investigate based on the underlying sensing mechanism. These results reveal new pathways in the biomedical application field for the analysis of exhaled breath, where H₂ indicates gastrointestinal diseases.