How humans make decisions is one of the primary domains of inquiry in psychology. Our ability to make decisions leads to direct consequences in our lives and defines one aspect of autonomous function. Among clinicians and researchers, the pursuit of effective cognitive enhancements and treatments that could directly or indirectly influence our decision processes has become widespread, since many of the neural circuits that we stimulate are involved in autonomous decision-making. Given rapid scientific developments, it is prudent to consider how neuromodulation could affect a person’s ability to make choices and manage trade-offs between decision outcomes. In light of this dilemma, we offer a framework based in decision neuroscience that separates brain networks into decision-making core, volitional action, and moderating systems. This framework bridges bioethics and cognitive neuroscience to provide heuristics for the neural basis of autonomous decision-making. In doing so, we provide a general call to predict and weight risks and benefits of different degrees and kinds with regard to decision-making as increasingly precise neuromodulation techniques emerge.