Lupin plants (Lupinus spp.) produce highly toxic compounds quinolizidine alkaloids (QAs), which have great pharmaceutical potential and prominent use in chemistry, but also hinder the use of protein-rich lupin seeds as food or feed. Knowledge of QA biosynthesis is limited, with only the first enzyme in the pathway, lysine decarboxylase (LDC), has been discovered so far. Here, we report the transcriptome of a high-QA content (bitter) variety of narrow-leafed lupin (L. angustifolius), obtained using 8 different tissues and 2 different sequencing technologies. In addition, we perform a co-regulation analysis using LDC, which yielded 33 genes that are highly co-expressed with this gene and that represent strong candidates for involvement in lupin alkaloid biosynthesis. One of these genes encodes a copper amino oxidase able to convert cadaverine into 1-piperideine as shown by heterologous expression and enzyme assays. Kinetic analysis of this enzyme revealed a low KM value for cadaverine, supporting a role in the QA pathway. Our transcriptomic dataset thus represents a crucial step towards the discovery of enzymes, transporters and regulators involved in lupin alkaloid biosynthesis.