Course-based Undergraduate Research Experiences (CUREs) are attractive solutions for scaling undergraduate research experiences at primarily undergraduate teaching institutions, where resources for faculty research activities can be limited. The Sustainable Interdisciplinary Research to Inspire Undergraduate Success (SIRIUS) project is a unique program that integrates CUREs, coordinated around a local real-world problem, throughout a biology department's curricula. The CUREs are scaffolded to provide all biology majors with multiple opportunities to engage in scientific investigations as they advance through introductory, intermediate, and advanced courses. In this mixed methods, cross-sectional study, we explore students' perceptions of the authenticity of their experiences as they progress through the SIRIUS CUREs. Triangulated data collected from two instruments indicated that students in advanced courses recognized more involvement in research activities and perceived greater authenticity in the science they were performing compared with introductory and intermediate students. Intermediate and advanced students perceived more opportunities for independence; however, experiences with failure and the influence these experiences had on the perceptions of authenticity was primarily observed with advanced students. This study contributes to the growing literature on CUREs with a focus on students from a primarily undergraduate institution with multiple minority-serving designations.