National efforts to transform undergraduate biology education call for research experiences to be an integral component of learning for all students. Course-based undergraduate research experiences, or CUREs, have been championed for engaging students in research at a scale that is not possible through apprenticeships in faculty research laboratories. Yet there are few if any studies that examine the long-term effects of participating in CUREs on desired student outcomes, such as graduating from college and completing a science, technology, engineering, and mathematics (STEM) major. One CURE program, the Freshman Research Initiative (FRI), has engaged thousands of first-year undergraduates over the past decade. Using propensity score--matching to control for student-level differences, we tested the effect of participating in FRI on students' probability of graduating with a STEM degree, probability of graduating within 6 years, and grade point average (GPA) at graduation. Students who completed all three semesters of FRI were significantly more likely than their non-FRI peers to earn a STEM degree and graduate within 6 years. FRI had no significant effect on students' GPAs at graduation. The effects were similar for diverse students. These results provide the most robust and best-controlled evidence to date to support calls for early involvement of undergraduates in research.