Motivation is a key factor in promoting students' active engagement in regular physical activity. According to self-determination theory -- one of the prominent motivational theories -- for this to occur, students' basic psychological needs must be met (i.e., their need for autonomy, competence and relatedness). Students' self-determined motivation may be further amplified by using evidence-based pedagogical practices, such as instructional alignment. Such information may be particularly valuable for college and university physical activity instructors who are sometimes experts in their activity, but who may have little formal training in motivational theory or evidence-based pedagogical strategies. In this article, we describe the concept of instructional alignment and discuss how college and university physical activity instructors, in particular, can integrate this knowledge into their courses with the intent being to enhance their students' satisfaction of basic psychological needs and long-term physical activity motivation. Multiple practical applications are shared.