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Active learning pedagogies such as inquiry-based learning have the potential not only to improve students’ science literacy but also promote affective learning and interest in science, technology, engineering, and mathematics (STEM) careers. Moreover, a focus on affective learning may be key to improve recruitment in STEM. Yet, we know little about how participation in inquiry-based courses can impact college students’ affective learning. Here, we present results from a comparative analysis of two affective learning outcomes, attitudes toward science and science identity, after participation in inquiry-based laboratory courses. Then, we synthesize what we have learned about successes and limitations to promoting growth in positive attitudes toward science and science identity after participation in these courses. Our work focuses on non-science majors who are deaf, hard-of-hearing and hearing signers in bilingual (American Sign Language and written English) inquiry-based biology laboratory courses. We concentrate on the Deaf Community because deaf individuals often face challenges regarding access in STEM education. Our results indicate that participation in inquiry-based laboratory courses has the potential to positively influence students’ attitudes toward science via repeated engagement with hands-on, student-driven experimentation, peer collaboration, and a welcoming classroom environment. However, participation in these classes had a limited impact on students’ science identities. Some students saw themselves as scientists during laboratory classes, however, their science identities beyond the classroom remained unchanged. While inquiry-based laboratories successfully promote one aspect of affective learning, work is needed to improve students’ science identities and increase interest in STEM careers to more effectively recruit students in these courses.