Due to excellent separation capacity for complex mixtures of chemicals, comprehensive two-dimensional gas chromatography (GC × GC) is being utilized with increasing frequency for metabolomics analyses. This review describes recent advances in GC × GC method development for metabolomics, organismal sampling techniques compatible with GC × GC, metabolomic discoveries made using GC × GC, and recommendations and best practices for collecting and reporting GC × GC metabolomics data. •The excellent separation capacity of GC × GC is well suited for metabolomics.•Methods are being developed to optimize metabolome sampling and analysis.•GC × GC metabolome analyses are moving toward identifying mechanisms.•Data reporting recommendations are provided to optimize data sharing via new metabolomics databases.•Best practices for GC × GC metabolomics analyses are described.