Academic Motivation Scale-Chemistry (AMS-Chemistry), an instrument based on the self-determination theory, was used to evaluate students' motivation in two organic chemistry courses, where one course was primarily lecture-based and the other implemented flipped classroom and peer-led team learning (Flip-PLTL) pedagogies. Descriptive statistics showed that students in both courses were more extrinsically motivated and their motivation moved in negative directions across the semester. Factorial multivariate analysis of covariance revealed a main effect of pedagogical approach. Students in the Flip-PLTL environment were significantly more motivated toward chemistry at the end of the semester while controlling for the motivation pre-test scores; however, there was no evidence for a sex main effect or an interaction effect between sex and pedagogical approach. Correlation results revealed variable relationships between motivation subscales and academic achievement at different time points. In general, intrinsic motivation subscales were significantly and positively correlated with student academic achievement; "Amotivation" was negatively correlated with academic achievement. The findings in this study showed the importance of Flip-PLTL pedagogies in improving student motivation toward chemistry.