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This mixed-methods study assessed students’ perceptions (N=354) of biology learning environments at a historically black university in the USA. Perceptions were compared between year one and two of the study, and actual perceptions were compared with what students would prefer. Also, students’ attitudes and self-efficacy were assessed. Statistically significant differences between actual and preferred means were found for six of seven scales. Effect sizes were high (0.67-1.14). The narrowest gap between actual-preferred scales was for Cooperation while the widest gap was for Clarity of Assessment Criteria. Differences between the two years were not statistically significant indicating that more time is needed before instructional changes can be seen. Many suggestions for creating a more active learning environment were heard during interviews.