Alkaloids are a group of approximately 12,000 low molecular weight and nitrogenous secondary metabolites found in 20% of plant species. Their potent biological activity suggests that alkaloids function as defense compounds. Benzylisoquinoline alkaloids (BIAs) are derived from tyrosine and are diversified by an intricate biochemical network of intramolecular coupling, reduction, methylation, hydroxylation, and other reactions to generate the estimated 2500 known structures. Several BIAs are used directly as pharmaceuticals or serve as precursors for the synthesis of semi-synthetic drugs. Plants remain the only economical source for the production of compounds such as morphine and codeine owing to their chemical complexity, which makes de novo synthesis challenging and costly. Much research has been directed toward understanding the biosynthesis of the BIAs and manipulating source plants to increase production of key products and pathway intermediates. However, metabolic engineering experiments often yield unexpected results demonstrating the need for an improved perspective on the biochemistry, regulation, and cell biology of BIA pathways. This review summarizes recent advances in the establishment of predictive metabolic engineering within the context of plant alkaloid biosynthesis.