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Humans are characterized by their ability to leverage rules for classifying and linking stimuli to context-appropriate actions. Previous studies have shown that when humans learn stimulus-response associations for two-dimensional stimuli, they implicitly form and generalize hierarchical rule structures (task-sets). However, the cognitive processes underlying structure formation are poorly understood. Across four experiments, we manipulated how trial-unique images mapped onto responses to bias spontaneous task-set formation and investigated structure learning through the lens of incidental stimulus encoding. Participants performed a learning task designed to either promote task-set formation (by “motor-clustering” possible stimulus-action rules), or to discourage it (by using arbitrary category-response mappings). We adjudicated between two hypotheses: Structure learning may promote attention to task stimuli, thus resulting in better subsequent memory. Alternatively, building task-sets might impose cognitive demands (for instance, on working memory) that divert attention away from stimulus encoding. While the clustering manipulation affected task-set formation, there were also substantial individual differences. Importantly, structure learning incurred a cost: spontaneous task-set formation was associated with diminished stimulus encoding. Thus, spontaneous hierarchical task-set formation appears to involve cognitive demands that divert attention away from encoding of task stimuli during structure learning.