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Abstract Background Achievement motivation research has established that motivational factors predict academic affect, cognition, and behavior. Recent studies have shown that trait mindfulness might also predict these academic outcomes. However, it remains unclear whether trait mindfulness has incremental validity over motivational factors. We hypothesized that trait mindfulness would explain unique variance in academic outcomes beyond motivational factors, because mindfulness that is characterized by the being mode of mind (i.e., a present-focused, non-striving, and accepting mind mode) would contribute to academic outcomes through unique and effective self-regulatory processes (i.e., bottom-up self-regulation of learning and present-focused, acceptance-based self-regulation of academic stress), which differ from those (i.e., top-down self-regulation of learning and future-focused, change-oriented self-regulation of academic stress) promoted by motivational factors that are characterized by the doing mode of mind (i.e., a goal-oriented, striving, and change-seeking mind mode). We tested the hypothesis by examining four established motivational factors (competence perception, implicit theory of intelligence, achievement goals, and autonomous and controlled academic reasons) and five outcome variables (test anxiety, enjoyment of learning, study strategy, mind-wandering, and help-seeking avoidance) that had been investigated in both the trait mindfulness and achievement motivation literatures. Methods One hundred and seventy-five students (104 females) were recruited from undergraduate psychology and cultural studies classes at two universities in Japan. Trait mindfulness was assessed using the Five Facet Mindfulness Questionnaire. The other study variables were assessed using established measures as well. We conducted hierarchical multiple regression analyses to test the hypothesis. Results Trait mindfulness predicted four of the five outcome variables (i.e., test anxiety, enjoyment of learning, mind-wandering, and help-seeking avoidance) after controlling for the motivational factors. The acting-with-awareness facet predicted three outcome variables, whereas the other facets predicted one outcome each. Conclusions This study supports the incremental validity of trait mindfulness relative to motivational factors, suggesting that not only the doing mode of mind but also the being mode is beneficial for academic learning.