Since hop secondary metabolites have a direct correlation with the quality of beer and other hop-based beverages, and the volatile fraction of hop has a complex composition, requiring effective separation, here we explore the application of headspace solid-phase microextraction as a sample preparation method, coupled with comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS) analysis. The methodology involved the use of a DVB/PDMS fibre with 500 mg of hop cone powder, extracted for 40 min at 50 °C, for both GC–MS and GC×GC–MS. The varieties Azacca, Cascade, Enigma, Loral, and Zappa were studied comprehensively. The results demonstrate that GC×GC–MS increases the number of peaks by over 300% compared to classical GC–MS. Overall, 137 compounds were identified or tentatively identified and categorised into 10 classes, representing between 87.6% and 96.9% of the total peak area. The composition revealed the highest concentration of sesquiterpene hydrocarbons for Enigma, whilst Zappa showed a relatively significant concentration of monoterpene hydrocarbons. Principal component analysis for all compounds and classes, along with hierarchical cluster analysis, indicated similarities between Zappa and Cascade, and Azacca and Loral. In conclusion, this method presents an optimistic advancement in hop metabolite studies with a simple and established sample preparation procedure in combination with an effective separation technique.