Does plant ecology have a “net-effect” problem? Net effects are expressed in metrics such as biomass or density that identify an important overarching effect but are produced by a suite of subtle, interacting, and usually unidentified factors, or processes, that vary in intensity. Measuring net effects has led to groundbreaking discoveries in ecology. However, when the relative contributions of subtle interacting processes vary, so do net effects, potentially leading to conflicting conclusions about underlying mechanisms and processes which stymie integration and generalization. To illustrate how unpacking net effects might enable generalization, we review the development of the stress gradient hypothesis, where the processes underpinning net effects are often conceptually incorporated, and then key innovations in the field of biodiversity–ecosystem functioning relationships. We then consider how unpacking net effects has enabled progress in the study of intercropping and could contribute to ecological restoration. Finally, we identify where further unpacking of net effects can contribute to addressing apparent paradoxes, and potential experimental approaches to help with this challenge. Measuring net effects has enabled tremendous progress in ecology; but strategically unpacking net effects will improve our ability to generalize more effectively across ecosystems and species.