The purpose of this study was to examine whether Socioscientific Issues (SSI) based learning environments affect university students' epistemological understanding of scientific inquiry differently from traditional science educational contexts. We identify and compare conceptions of scientific inquiry of students participating in an interdisciplinary, SSI-focused undergraduate human biology major (SSI) and those participating in a traditional biology major (BIO). Forty-five SSI students and 50 BIO students completed an open-ended questionnaire examining their understanding of scientific inquiry. Eight general themes including approximately 60 subthemes emerged from questionnaire responses, and the numbers of students including each subtheme in their responses were statistically compared between groups. A subset of students participated in interviews, which were used to validate and triangulate questionnaire data and probe students' understanding of scientific inquiry in relation to their majors. We found that both groups provided very similar responses, differing significantly in only five subthemes. Results indicated that both groups held generally adequate understandings of inquiry, but also a number of misconceptions. Small differences between groups supported by both questionnaires and interviews suggest that the SSI context contributed to nuanced understandings, such as a more interdisciplinary and problem-centered conception of scientific inquiry. Implications for teaching and research are discussed.