Ecological processes can have strong effects on production systems, many of which prevent crops from reaching their maximal yield. Past and present management strategies have been developed to mitigate the negative interactions, thereby improving crop production. However, when applied to complex and variable agroecosystems, some of these strategies have resulted in unintended ecological effects that ultimately hindered production. Transgenic crops are a widespread and powerful management option, and there is a tremendous need to understand their intended ecological effects as well as potential unintended direct and indirect effects. The purpose of this review is threefold: (1) to discuss four of the major ecological effects that limit crop production: competition, herbivory, disease, and abiotic stresses, (2) to describe how biotechnology is addressing these problems, and (3) to examine the ways these biotechnological solutions may cause ecological effects that unintentionally hinder crop production. We find that, to date, there has been little diversity in the types of transgenic crops available and the approaches they use to improve crop production. Transgenic crops, like previous agricultural technologies, are designed to enhance a singular plant trait in order to solve a specific production problem.When viewed in a simplified system, transgenic crops seem to provide effective means to mitigate negative ecological effects. However, when approached via a larger ecological context, it is clear that transgenic crops have already had and will continue to have unintended ecological effects that can ultimately affect crop production through mechanisms such as gene flow, resistance evolution, community interactions, and production practices. No management option, including transgenics, is universally beneficial or detrimental. The ecological context of specific agroecosystems may improve predictions of the benefits, limitations, and consequences of a given management tactic within that system. As we increase our understanding of the ecological context of crop production problems, we may be able to improve our control efforts to maximize production and minimize potential problems in the future.