The present study examined the interplay between self-determined motivation and the use of cognitive strategies in predicting university students' academic performance while taking into account the effect of prior achievement. A theory based model was tested using structural equation modeling on a sample of 764 Italian university students. Results showed that prior achievement influenced students' academic performance and their motivation and use of cognitive strategies. Critical thinking was the only cognitive strategy which proved to have a significant impact on students' academic performance. Autonomous motivation had an indirect positive impact on academic performance through its influence on the critical thinking strategy. Controlled motivation had a direct negative impact on academic performance. On the whole, our findings suggest that autonomously motivated students tend to achieve better academic performance by using critical thinking, while students who are driven by controlled motivation have lower academic performance.