The quantitative insight in processes underlying yield and concentrations of interesting secondary metabolites in crops is still limited. Yet, this insight is essential to further improve crops and commercial production of target metabolites. Artemisia annua L. (annual or sweet wormwood, Asteraceae) was used to conceptualize a model to describe the processes determining and limiting the production of target metabolites during crop growth. A. annua is an annual herb producing the antimalarial artemisinin, a sesquiterpene lactone with an endoperoxide bridge. Artemisinin is predominantly produced in glandular trichomes present on the leaves and inflorescences. Leaves are the most important organs harvested in commercial production. The accumulation of artemisinin in the crop was analysed as the resultant of the key processes determining leaf dry weight production, accumulation of artemisinin in the leaves and losses after synthesis. A yield formation modelling approach was used to quantify artemisinin yield as a function of the individual processes and to study which processes limited production. Leaf dry weight production was limited by low total dry matter production of the crop because of poor radiation interception during early canopy expansion, and by a high proportion of dry matter allocated to stems that do not contribute to artemisinin production. Production of the target metabolite in the leaves was limited because the total production of artemisinin precursors per unit leaf dry weight was low and because the conversion of precursors to artemisinin was only partial. Possibilities to increase the values of the different yield components are discussed. A new, simple, model for explaining variation in artemisinin yield based on leaf and trichome production in combination with biosynthesis of artemisinin is proposed.