Student cognition and motivation, as well as institutional policies, determine student course grades and retention in science, technology, engineering, and mathematics (STEM) majors. Regarding cognition, study skills relate to course grades, and grades relate to retention in STEM. Several aspects of motivation are related to both grades and retention in STEM: self-efficacy (self-confidence for completing assignments), continuing interest in learning more about the subject, and effort control (remaining focused on classes and studying). Students’ cognition and motivation are interdependent, and, furthermore, they play out in the context of multiple institutional policies, such as academic support centers, career counseling, financial aid policies, forced curving of course grades, course timing, and course registration policies. All of these interdependent factors can improve with targeted programs that complement each other. Some challenges for reform include instructor resistance to changing teaching and a lack of coordination, or even competing emphases, among university policies and resources, such as course scheduling, academic support, advising, career counseling, and financial aid.