The potential for financial conflicts of interest (COIs) to influence scientific research has become a significant concern. Some commentators have suggested that the development of standardized study protocols could help to alleviate these problems. This paper identifies two problems with this solution: (1) scientific research incorporates numerous methodological judgments that cannot be constrained by standardized protocols; and (2) standardization can hide significant value judgments. These problems arise because of four weaknesses of standardized guidelines: incompleteness, limited applicability, selective ignorance, and ossification. Therefore, the standardization of study designs should not serve as an alternative to addressing the interests and power relations that pervade science policy-making. Policy makers should take at least two steps to prevent powerful interest groups from co-opting standardized guidelines. First, their development and review should be made as transparent as possible and should be subjected to broadly-based deliberation. Second, standardized guidelines should be supplemented with efforts to scrutinize the conditions under which financial COIs tend to have the most worrisome effects so that additional steps can be taken to eliminate and mitigate those conditions.