Integrated weed management in commercial wheat production is urgently needed due to increasing herbicide resistance and production costs. Benzoxazinoids (BXs), which include benzoxazinones and benzoxazolinones, are unique bioactive metabolites produced by certain members of the Poaceae including maize, wheat, rye and some dicots. BXs play important roles in plant defence and are causal agents of allelopathic interference. We investigated the role of genetics, environment and crop growth stage on BX abundance in the roots and rhizoplane of selected commercial wheat cultivars, and quantified their microbial transformation products (aminophenoxazinones) in roots and rhizosphere soils. Methods: Cultivar trials of competitive wheat (Triticum aestivum L.) genotypes were conducted in two moderate to low rainfall (449–572 mm) locations in southeastern Australia in 2015 and 2016. Replicated shoot, root, rhizoplane, and rhizosphere soil samples were collected for metabolic profiling at selected crop phenological stages, extracted and further analysed for known benzoxazinoid metabolites by liquid chromatography coupled with high resolution mass spectrometry. Results: Fifteen BXs and related microbially derived aminophenoxazinones were detected in wheat shoots, roots, rhizoplanes and rhizosphere soils in both years and locations. MBOA, HMBOA and HMBOA-Glc were the three most abundant BX metabolites in wheat tissues, with the heritage cultivar Federation producing the highest levels of MBOA. The phytotoxic aminophenoxazinones APO and AMPO were the most abundant BX microbial transformation products and were detected in wheat roots, rhizoplanes and rhizospheres. Abundance varied with cultivar, growth stage, location and year. Conclusions: Microbially-produced aminophenoxazinones generated from both heritage and modern wheat root exudates were detected and quantified in rhizosphere soils, with abundance dependent on cultivar, growth stage, and season. Concentrations of microbial metabolites APO, AMPO, and AAPO were higher in the rhizosphere of young wheat seedlings in contrast to that of mature plants suggesting that phenoxazinone production was upregulated early in the season. Our findings demonstrate that BX metabolites at all life stages of wheat potentially undergo rapid biotransformation to aminophenoxazinones under field conditions, resulting in ecologically relevant concentrations sufficient for weed suppression by certain wheat cultivars.