Field experiments determined copper and zinc content and accumulation in yellow lupine roots, stems, leaves, flowers, pods and seeds. The test factors included development stages (BBCH 65 and BBCH 90) at which harvest was performed as well as nitrogen doses (0, 30, and 120 kg·ha−1) introduced to the soil prior to sowing. A higher copper content (by an average of 20.9%) and zinc content (by 53.7%) were obtained in the whole mass of lupine harvested at the flowering stage compared to that at the full maturity stage. Yellow lupine fertilised with 120 kg N·ha−1 contained and took up more copper and zinc than both lupine cultivated without nitrogen fertilization and fertilised with 30 kg N·ha−1. The application of different nitrogen doses had no significant effect on the contents of the micronutrients in the seeds of the test plant. The amount of copper and zinc accumulated in the seeds was the largest following the application of 120 kg N·ha−1. Lupine accumulated the largest amounts of both elements in the leaves irrespective of the development stage at which the harvest was carried out. The bioaccumulation factor for copper and zinc was higher in the lupine harvested at the flowering stage than in the lupine harvested at full maturity, but it was not significantly determined by the applied nitrogen fertilization. The values of translocation coefficient for the tested heavy metals, usually higher than 1, indicate significant potential for their accumulation in yellow lupine biomass. Under conditions of an increased zinc content in the soil, lupine green matter harvested at the flowering stage contained an above-standard amount of this heavy metal and could not be used for animal feed.