Metabolomics encompasses the acquisition of large-scale datasets from a single sample to identify and/or elucidate physiological or pathological mechanisms, or even to assess environmental exposure, being sample preparation and instrumental analysis two fundamental steps in the construction of a metabolomics workflow. The study of the human exhaled breath condensate (EBC) has gained tremendous interest recently owing to the advances in analytical techniques. Thus, this study aims to develop a methodology for EBC metabolites profiling based on headspace solid phase microextraction (SPME) combined with comprehensive two-dimensional gas chromatography (GC × GC). Metabolite’s extraction efficiency was improved by the optimization of four SPME parameters using a real EBC matrix: fibre coating, sample pH and volume, and extraction temperature. EBC analysis was performed according to the optimized parameters, using aliquots of 500 μL of EBC, at its physiological pH, with the DVB/CAR/PDMS fibre coating, at 40.0 ± 0.1 °C, being able to detect analytes at pg/mL, with acceptable reproducibility. EBC volatile composition was provided, with around 400 chemical features detected, in which 130 were putatively identified as belonging to hydrocarbons, aldehydes, alcohols, ketones, esters, monoterpenic and sesquiterpenic compounds, ethers, norisoprenoids and furans, revealing therefore its high complexity. This research represents the most detailed study on the volatile composition of EBC and allows the assessment of a broad range of endogenous and exogenous metabolites, with further relevance on clinical or environmental exposure studies. To test the applicability of this methodology, an exploratory study was carried out to assess the impact of the use of surgical facemasks on young researcher’s lipid peroxidation volatile markers during a normal working day in a laboratory. In young healthy adults (age ≤ 32), the use of surgical facemasks seems not significantly affect the levels of the volatile markers of lipid peroxidation (aliphatic alkanes and aldehydes), neither the O2 saturation level - SpO2. This methodology shows promise as a convenient way to follow specific physiological or pathological conditions based on EBC metabolome and may be paired as part of an aggregate analytical structure.