With respect to the current hypothesis that natural amino acids may serve as starting material for the biosynthesis of alkyl-methoxypyrazines, the enantiomeric distribution of the potent aroma compound 3-sec-butyl-2-methoxypyrazine (SBMP) was determined in various species using heart-cut multidimensional gas chromatography (H/C MDGC) or comprehensive two-dimensional gas chromatography (GC × GC). Complementary to an earlier described separation on octakis-(6-O-methyl-2,3-di-O-pentyl)-γ-cyclodextrin used as chiral stationary phase, we found a reversal of the elution order of SBMP enantiomers on heptakis-(2,3-di-O-methyl-6-O-tert-butyldimethylsilyl)-β-cyclodextrin, providing further confirmation options for that type of analysis. Optimization of the enantioseparation of SBMP in a single-oven H/C enantio-MDGC system involved the use of a dual-jet cryo modulator for trapping of analytes transferred from the achiral (1)D column to the chiral (2)D column before starting the (2)D enantioseparation with an independent temperature ramp. For the enantiodifferentiation by enantio-GC × GC, the modulation period had to be significantly shortened to avoid loss of chiral resolution gained in (1)D. H/C MDGC with mass spectrometric detection (MS) using selected ion monitoring (SIM) was sufficient for parts per billion level analysis, whereas H/C MDGC-MS/MS or GC × GC time-of-flight (TOF) MS were necessary for parts per trillion level analysis. In various vegetables, lady beetles and Vitis vinifera species analyzed, only (S)-SBMP was detected, supporting the hypothesis of natural amino acids serving as starting material for the biosynthesis of alkyl-methoxypyrazines.