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This study investigated students’ reasoning of non-covalent interactions and their transfer of learning under two different instructional sequences. The instruction first approach (I-PS) asserts explicit instruction should precede problem-solving activities to avoid cognitive overload, whereas the problem-solving first approach (PS-I) argues that students should solve problems before instruction to better prepare their future learning. To resolve this tension, this study used think-aloud and semi-structured interview data to explore the unpredicted affordances of the two approaches from a learner’s perspective. Our findings showed that, with a medium prior knowledge, the PS-I learners generated more connections between knowledge elements than the I-PS learner. This result highlights a unique benefit of the PS-I approach that would have been missed with traditional transfer assessments.