For molecular farming applications, the capacity to transform perennial plants for recombinant protein production gives access to stable and almost perpetual production of pharmaceuticals from a single population of plants. Being able to produce a bioactive protein with a uniform and well characterised population not only reduces production costs but more importantly, it ensures even and predictable production rate of a uniform product from a genetically stable population. Despite their promising potential, two main hurdles hindered the early development of perennial plant‐based expression systems: the lack of adapted expression cassettes and the difficulty to genetically transform and regenerate the best‐suited perennials. This chapter describes recent scientific breakthrough in alfalfa transformation and protein expression and purification that opened the way to the development of an efficient recombinant protein production platform using alfalfa as bioreactor.