In this study we use data from the Programme for International Student Assessment (PISA) to investigate the effect of teachers' motivation on students' scientific literacy and motivation in Colombia. These relationships are explored using a multilevel modeling framework and through the lens of Self-Determination Theory. Although difficulties in achieving education quality in developing and emerging economies are commonly attributed to teacher motivation issues, and important policy measures are implemented based on this assumption, this topic remains largely empirically unexplored. The purpose of the study is to contribute to fill this gap and provide empirically based insights for a broader and more informed dialogue regarding the effect of motivation in the development of scientific literacy, and to the design and implementation of evidence-based policies, instructional practices, and interventions. In this analysis, we did not find a significant relationship between teacher motivation and either students' scientific literacy or motivation. However, students' interest in science and sense of self-efficacy were significantly associated with their own achievement. The results also show that teacher-directed instruction is the strongest predictor of scientific literacy as opposed to inquiry-based teaching. However, inquiry-based teaching was found to be a positive predictor of increased students' motivation.