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This study examined the effects of learner choice and concept map format on chemistry learning outcomes in an undergraduate course. Using a 2 (choice vs. no-choice) × 3 (format: translation, fill-in-the-blank, correction) factorial design, with perceived competence as a covariate, 621 students engaged in concept maps followed by retention and transfer assessments. Results showed significant main effects of choice and concept map format on retention; the choice group outperformed the no-choice group, and map translation produced better retention. For transfer, only the concept map format yielded a significant main effect, favoring the map translation condition. Findings suggest that structured autonomy and cognitively demanding tasks promote retention when aligned with learner competence. Practical implications are discussed.