Motivation is an integral factor in substance use treatment and long-term recovery. However, it is unclear what role intrinsic and extrinsic motivation play across different treatment modalities. A meta-analysis (N = 84) was performed to estimate the pooled effect size of Motivational Interviewing (MI; primarily targeting intrinsic motivation) and contingency management (CM; primarily targeting extrinsic motivation) at different follow-up periods. Collapsed across all substance types, CM had a significant effect at 3-month follow-up, only. In contrast, MI had a significant effect at 6-month follow-up, only. CM had small and medium effects on multiple substances at 3-month follow-up (i.e., tobacco, marijuana, stimulants, polysubstances), but not at 6-month follow-up. MI had 1 significant medium effect at 3-month follow-up (i.e., marijuana), but several significant small effects at 6-month follow-up (i.e., alcohol, tobacco, polysubstances). This meta-analysis suggests that both CM and MI promote reductions in a range of substances, even several months after the intervention concludes. Further, these results provide some evidence that extrinsically focused CM may produce medium follow-up effects in the short run, but intrinsically focused MI may produce small but durable follow-up effects. However, this interpretation is complicated by the differences between the MI and CM studies that preclude statistical tests comparing effect sizes, and few studies assessed motivation itself. Future researchers should investigate how motivational dynamics impact lasting outcomes in substance use treatment.