The severity of brown spot caused by the fungus Pleiochaeta setosa (Kirchn.) Hughes in narrow-leafed lupin (Lupinus angustifolius L.) is reduced by improving phosphorus (P) nutrition and using agronomic treatments that extend crop rotation or increase cereal stubble retention. The aim of this work was to investigate the impact of these treatments on the alkaloid concentrations of the harvested seed of 3 sweet cultivars of L. angustifolius that differed in their susceptibility to this fungal disease: Merrit (susceptible), Tallerack and Myallie (both moderately resistant). Because abiotic and biotic stresses appear to stimulate plant alkaloid biosynthesis, we hypothesised that higher levels of disease pressure may increase alkaloid concentrations in the harvested seed, particularly in the disease-susceptible Merrit.The main effects of P nutrition, cereal stubble retention, genotype and crop rotation were significant for the severity of brown spot and plant biomass of narrow-leafed lupin in a field trial in Wongan Hills, Western Australia, but were not significant for total alkaloid concentrations or the relative proportions of individual alkaloids of the harvested seed. Seed total alkaloid concentrations were in most cases below the maximum permitted concentration established for lupin seed (200 mg/kg dry matter) and were independent of the severity of brown spot on leaves. The great fluctuations of seed total alkaloid concentrations observed in grower deliveries to bulk handling facilities and in lupin cultivar yield testing trials are unlikely to result from the nutritional and agronomic treatments such as those investigated in this experiment, or the various disease levels that resulted from these treatments.