Yield and harvest index of narrow-leafed lupin (Lupinus angustifolius L.) are variable, and factors affecting their reliability have not been clearly identified. In this study, plants were grown in sand culture and were non-nodulated and supplied with mineral nitrogen (N) or acquired N through symbiotic N-2 fixation. Transient N deficiency was imposed a number of times during development in nodulated plants by hushing pure O-2 to the roots to suppress N-2 fixation and in non-nodulated plants by changing the rate of N addition. Low N supply (0.4 mM) before floral initiation or for 2 weeks during floral initiation caused a reduction in seed yield. Transient N deficiency induced by O-2 flush during early growth (Weeks 6 and 7 after sowing) had a marked effect on vegetative growth, the number of main stem flowers, pod set, and seed yield. The early N deficiency also affected shoot and root N concentrations and total cytokinin concentrations in root exudate. Compared with N-2-fixing plants, those supplied with adequate mineral N had a greater flower number and greater branch growth and biomass, but not higher pod set and seed yield, resulting in lower harvest index. Seed N concentrations were also decreased by transient N deficiencies at early (floral initiation), mid (flowering), and late (grain,filling) stages. These findings indicate that any field conditions which transiently reduce N-2 fixation (e.g. temporary waterlogging or drought) are likely to result in lower grain yield and quality of lupin crops.