Breath gas profiles, which reflect metabolic disorders like diabetes, are the subject of scientific focus. Nevertheless, profiling is still a challenging task that requires complex and standardized methods. This study was carried out to verify breath gas patterns that were obtained in previous proton-transfer reaction-quadrupole mass spectrometry (PTR-QMS) studies and that can be linked to glucose metabolism. An experimental setup using simultaneous PTR-QMS and complementary highly time-resolved needle trap micro extraction (NTME) combined with comprehensive 2D gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS) was established for the analysis of highly polar volatile organic compounds (VOCs). The method was applied to the breath gas analysis of three volunteers during a glucose challenge, whereby subjects ingested a glucose solution orally. Challenge responsive PTR-QMS target VOCs could be linked to small n-carbonic (C2-C4) alcohols and short chain fatty acids (SCFA). Specific isomers could be identified by simultaneously applied NTME-GC×GC-TOFMS and further verified by their characteristic time profiles and concentrations. The identified VOCs potentially originate from bacteria that are found in the oral cavity and gastrointestinal tract. In this study breath gas monitoring enabled the identification of potential VOC metabolites that can be linked to glucose metabolism.