Attempts by politicians to control bureaucratic decisions include both structural (how is the agency making the decision organized?) and procedural (what rules must they follow when making the decision?). But how do these two modes of influence interact? This article examines the interaction between bureaucratic structure and one procedural control, the requirement that agencies conduct an analysis of their decisions prior to their issuance. I look at this interaction in the context of two types of analysis, cost-benefit analysis and environmental impact assessment. I interview 16 individuals in each field and draw from their experiences of conducting and reviewing more than a thousand analyses. The conduct of analysis is affected by where analysts are placed in agencies. In particular, independence of analysts has a trade-off. The more independent analysts are, the more likely they can challenge preferred decisions in their agency. But independent analysts are brought into decisions later and their independence may limit their long-term impacts on agency culture. Despite this trade-off, analysts expressed a clear preference for independence. The interaction between different controls of bureaucratic behavior is a potentially fruitful line for further research.