The formation and storage of plant natural products such as phenylpropanoids, terpenoids and alkaloids are dynamic and complex processes that involve multiple subcellular compartments and cell types. Evidence is emerging to show that consecutive enzymes of phenylpropanoid and flavonoid biosynthesis are organized into macromolecular complexes that can be associated with endomembranes, that monoterpenoid biosynthetic enzymes are exclusively localized to highly specialized glandular trichome secretory cells and that complex monoterpenoid indole- and morphinan alkaloids require a combination of phloem parenchyma, laticifers and epidermal cells for their synthesis and storage. Highly ordered, protein-mediated processes that involve intra- and intercellular translocation need be considered when attempting to understand how a plant can regulate the formation and accumulation of complex but well-defined natural product profiles.