A principle of biorefining is extended to medicinal plants with the view of developing a more sustainable business model for biomass producers and extractors. This is demonstrated for Artemisia annua L. currently cultivated or harvested in the wild for extraction of a single compound, artemisinin, comprising on average 1 wt% dry weight of the plant biomass. We scaled extraction of artemisinin by a non-toxic to bacterial fermentation solvent tetrafluoroethane to a 5 L pilot scale. We identified a number of co-metabolites that could be extracted from the plant along with artemisinin and describe the multi-step extraction-fractionation sequence that potentially could be transferred to a large-scale multi-step extraction process. We also show possible routes to higher-value compounds on the basis of A. annua secondary metabolites, exemplified by the conversion of flavonoids to monomers.