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The present study investigated student learning profiles in a naturalistic classroom setting during scaffolded instruction on scientific topics of social relevance (e.g., the climate crisis). Using a theoretical framework that emphasizes scientific thinking and reasoning through critical evaluation, we measured students' evaluations of connections between scientific evidence and explanatory models, plausibility judgments about alternative explanations, and knowledge construction. Latent Profile Analysis (LPA) identified three distinct profiles: low prior knowledge, medium prior knowledge, and high prior knowledge. Results suggested that the medium prior knowledge profile showed positive shifts in plausibility judgments and knowledge, supporting the effectiveness of instructional scaffolding. The findings inform on how scaffolded instruction can enhance the teaching of scientific topics of social relevance.