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Evaluation of plausible alternative explanations of scientific phenomena is an authentic scientific activity. Instructional scaffolding can facilitate students’ engagement in such evaluations by facilitating their reflections on how well various lines of scientific evidence support alternative explanations. In the present study, we examined two forms of such scaffolding, with one form providing more autonomy support than the other, to determine whether any differential effects existed between the two. Nearly 300 adolescent students in middle school, high school, and university courses completed two activities on scientific topics of social relevance (e.g., the climate crisis, fossils and fossil fuel use, water resources, and astronomical origins), with the less autonomy-supportive form being completed prior to the more autonomy-supportive form. In line with prior pilot studies, both scaffold types demonstrated significant pre- to post-instructional shifts in plausibility judgments toward the scientific model and gains in knowledge with small to medium effect sizes. A mediation model provided a robust replication of previous findings showing that the indirect path meaningfully linked greater levels of evaluation to more scientific plausibility judgments and topic knowledge, above and beyond the direct relational path linking greater levels of evaluation to topic knowledge. However, we found no difference in relations between the two scaffold types, counter to our hypothesis that the more autonomy-supportive version would lead to better outcomes. This suggests that the implementation of more autonomy-supportive learning environments is conditional, opening up a promising avenue for additional research (e.g., looking at specific contexts and how activities should be sequenced to optimize learning).