Allohexaploid wheat (Triticum aestivum L.) is tolerant to halauxifen-methyl (HM) via rapid detoxification of the phytotoxic form of HM, halauxifen acid (HA), to non-phytotoxic metabolites. Previous research utilizing ‘Chinese Spring’ (CS) wheat, alien substitution (i.e., endogenous chromosome pair substituted with a homoeologous pair from diploid Sear’s goatgrass (Aegilops searsii M. Feldman & M. Kislev (AS)), or nullisomic-tetrasomic (NT) lines indicated plants lacking chromosome 5A are more sensitive to HM than CS. We hypothesized the increased HM sensitivity of these plants results from losing gene(s) on chromosome 5A associated with HA metabolism, which leads to a reduced HA detoxification rate relative to CS. To compare HA abundance among AS, CS, alien substitution and NT lines during a time course, two excised leaf studies using unlabeled HM and liquid chromatography-mass spectrometry analyses were performed. Aegilops searsii accumulated more HA than CS and each substitution line at 8, 12 and 24 h after treatment (HAT). Furthermore, only the wheat substitution line lacking chromosome 5A displayed greater abundance of HA relative to CS (2.4- to 3.8-fold, depending on the time point). In contrast, HA abundances in lines possessing chromosome 5A were comparable to CS at all points. When comparing NT lines to CS, the nullisomic 5D-tetrasomic 5A (N5D-T5A) line displayed similar HA abundance, whereas the nullisomic 5A-tetrasomic 5D (N5A-T5D) accumulated approximately three-fold more HA at 12 and 24 HAT. These results biochemically support the hypothesis that genes encoding HA-detoxifying enzyme(s) are located on wheat chromosome 5A and corroborate findings from previous greenhouse phenotypic experiments. Future experimentation is needed to identify and characterize genes and enzymes on wheat chromosome 5A involved with HA detoxification, which may include cytochrome P450 monooxygenases, unknown oxidases, UDP-dependent glucosyltransferases, or potentially transcription factors that regulate expression of these genes associated with HA detoxification.