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Socially relevant geoscience topics may be difficult for students to learn. For example, connecting hydraulic fracturing to Midwestern US earthquake swarms and using the fossil record to infer past Earth environments may challenge students because of their prior exposures to nonscientific explanations. Sociocognitive theoretical perspectives based on decades of developmental and educational psychology, as well as science education research posit that students may have particular difficulty in evaluating the connections between lines of scientific evidence and explanations. This challenge is especially daunting when students are confronted with various alternative explanations (e.g., scientific and nonscientific explanations). In the present study, we compared two types of scaffolds designed to facilitate Mid-Atlantic middle school students’ (N = 40) scientific thinking and learning about controversial geoscience topics when confronted with alternative explanations. In a less autonomy-supportive scaffold, participants were given four lines of evidence and two explanatory models, one scientific and one nonscientific. (Fracking; Supplementary Materials 1 & 2); in a more autonomy-supportive scaffold, students chose four of eight lines of evidence and two of three explanatory models, one scientific and two nonscientific (Fossils; Supplementary Materials 1 & 2). Quantitative analyses revealed that both activities facilitated students’ evaluations in shifting students’ judgments toward the scientific and deepening their knowledge, although the more autonomy-supportive activity had greater effect sizes. Structural equation modeling suggested that more scientific judgments related to greater knowledge at post-instruction for the more autonomy-supportive scaffold. These activities may help students develop more scientific evaluation skills, which are central to understanding geoscience content and science as a process.