Functional group taxonomy provides a powerful conceptual framework to classify and predict the chemical reactivity of molecular structures. These principals are most effective in monofunctional settings, wherein individual functional groups can be analyzed without complications. In more complex settings, the predictive value of these analyses decreases as alternative reaction pathways, promoted by neighboring substituents and aggregate molecular properties, emerge. We refer to this phenomenon as substrate-modified functional group reactivity. In this Perspective, we explain how substrate-modified functional group reactivity molded our synthetic routes to the hasubanan and acutumine alkaloids. These investigations underscore the potential for discovery and insight that can only be gained by studying the reactivity of complex multifunctional structures.