Modeling is a scientific practice that supports creative reasoning, motivates inquiry, and facilitates community sense-making. This paper explores students' perspectives on modeling in an undergraduate laboratory course, Authentic Inquiry through Modeling (AIM-Bio), in which they proposed, tested, and revised their own models. We conducted comparative case studies of eight students over a semester. Students described using models to support multiple forms of scientific reasoning and hypothesis generation. They recounted the challenges of dealing with uncertainty and integrating diverse ideas. They also described how these challenges pushed their thinking. Overall, students reported feeling a sense of scientific authenticity and agency through their modeling experience. We additionally provide an in-depth look at two students whose unique experiences in AIM-Bio emphasize the variable ways modeling can support inquiry learning. We claim that modeling emerged as a legitimate practice among students, because the AIM-Bio curriculum encouraged diversity in students' models, provided opportunities for students to grapple with uncertainty, and fostered collaboration between students. We suggest that biology educators consider how model-based inquiry can allow students to participate in science, as a way to support interest in, identification with, and ultimately persistence in science, technology, engineering, and mathematics fields.