We outline an instructional strategy for supporting students’ science literacy skills using a structured decision-making tool in an interdisciplinary undergraduate course. Instructional tools support basing complex socioscientific issues decisions on a reasoned analysis of tradeoffs among multiple conflicting values rather than heuristics, such as social norms. We explored the factors related to students’ decision-making about mountain lion management by examining if students’ value orientations, identity, or knowledge predicted their management decisions before, during, and after engaging in structured decision-making where they performed a tradeoffs analysis. We found that student decision-making may align more closely to students’ value orientations and identity at the beginning of the course, suggesting that by the end of the course, students were less likely to make decisions centered in social norms and simplified single-value heuristics. A structured decision-making tool can be an effective way to support students’ examination of value tradeoffs when solving complex socioscientific issues.