Lupins are used in animal feed because of their excellent nutritional composition. Australian and European Lupinus angustifolius seeds are incorporated in compound feed of calves for veal production in Belgium. To investigate the co-occurrence of quinolizidine alkaloids (QAs) and phomopsin A (PHO A) in lupin seeds and lupin-containing feed, and the potential transfer to animal-derived foods, representative samples were obtained from various actors in the chain. A UHPLC-MS/MS method was validated for the simultaneous quantification of seven QAs and PHO A in relevant matrices. Results indicate highly consistent total QA (TQA) levels in Australian lupins (173 ± 24 mg/kg) (n = 25), while European samples showed a high variability (1442 ± 1497 mg/kg) (n = 15). PHO A was detected in 7 of 40 samples. Lupin-containing feed had a mean TQA content of 42 ± 28 mg/kg (n = 20). An in vivo feeding trial demonstrated the transfer of QAs to muscle and liver of calves that were fed the lupin-containing feed. Highest concentrations were found for lupanine in liver tissue samples (67 ± 46 µg/kg). PHO A concentrations were below the LOD in all feed and tissue samples. These results indicate that animal-derived foods (veal meat/liver) are a potential route for QAs to enter the food chain.