The primary purpose of this study was to examine the ways in which a 12-week after-school science and engineering program affected middle school students' motivation to engage in science and engineering activities. We used current motivation research and theory as a conceptual framework to assess 14 students' motivation through questionnaires, structured interviews, and observations. Students reported that during the activities they perceived that they were empowered to make choices in how to complete things, the activities were useful to them, they could succeed in the activities, they enjoyed and were interested in the hands-on activities and some presentations, they felt cared for by the facilitators and received help when they were stuck or confused, and they put forth effort. Based on our examination of data across our three data sources, we identified motivating opportunities that were provided to students during the activities. These motivating opportunities can serve as examples to help both formal and informal science educators better connect motivation theory to practice so that they can create motivating opportunities for students. Furthermore, this study provides a methodological example of how students' motivation can be examined during the context of authentic science and engineering instruction.