One puzzle of President Obama’s presidency is why his stated commitment to criminal justice reform was not matched by actual progress. We argue that the Obama Administration’s failure to accomplish more substantial reform, even in those areas that did not require congressional action, was largely rooted in an unfortunate deference to the Department of Justice. In this Article, we document numerous examples (in sentencing, clemency, compassionate release, and forensic science) of the Department resisting common sense criminal justice reforms that would save taxpayer dollars, help reduce mass incarceration, and maintain public safety. These examples and basic institutional design theory all point in the same direction: real criminal justice reform requires putting the right institutions in charge of criminal justice policy making. This Article offers institutional changes that would help future Presidents make the system less punitive and reduce prison populations to achieve the broad transformation that Obama desired but did not attain. A critical move is to place criminal justice policy making in the hands of individuals who can advise the President independently of the institutional interests of prosecutors.