Narrow-leafed lupin (NLL) is a key grain legume crop in Australia that has recently gained recognition as a human health food. The grain is high in protein and dietary fibre whilst being low in fat and starch, and demonstrates a range of nutraceutical benefits. The value of the grain is however limited by the accumulation of quinolizidine alkaloids (QAs) – secondary metabolites which are unpalatable and sometimes toxic. Grain QA levels must remain below industry thresholds (<0.02%) in order to be used for food and feed purposes, however levels can vary considerably, sometimes exceeding these thresholds. Mechanisms of both QA production and environmental influence on this are poorly understood. This project makes use of newly available NLL genomic and transcriptomic data, in conjunction with molecular techniques, to identify and characterise genes involved in the biosynthesis of QAs. We have also developed a highly sensitive GC-MS/MS method for detecting NLL QAs, used to measure responses of QA production to environmental conditions in order to better understand how industry thresholds are exceeded. The findings from this project will serve to assist breeding programs and farmers to produce NLL grain that consistently meets QA thresholds, enhancing the value of a key Australian grain crop.