In this review, we consider and discuss the affinity and complementarity between a generic sample preparation technique and the comprehensive two‐dimensional gas chromatography process. From the initial technical development focus (e.g., on the GC×GC and solid‐phase microextraction techniques), the trend is inevitably shifting toward more applied challenges, and therefore, the preparation of the sample should be carefully considered in any GC×GC separation for an overreaching research. We highlight recent biomedical, food, and plant applications (2016–July 2020), and specifically those in which the combination of tailored sample preparation methods and GC×GC–MS has proven to be beneficial in the challenging aspects of non‐targeted analysis. Specifically on the sample preparation, we report on gas‐phase, solid‐phase, and liquid‐phase extractions, and derivatization procedures that have been used to extract and prepare volatile and semi‐volatile metabolites for the successive GC×GC analysis. Moreover, we also present a milestone section reporting the early works that pioneered the combination of sample preparation techniques with GC×GC for non‐targeted analysis.