With the rapid rise of generative AI in higher education and the unreliability of current AI detection tools, developing policies that encourage student learning and critical thinking has become increasingly important. This study examines student use and perceptions of generative AI across three proof-based undergraduate mathematics courses: a first-semester abstract algebra course, a topology course and a second-semester abstract algebra course. In each case, course policy permitted some use of generative AI. Drawing on survey responses and student interviews, we analyze how students engaged with AI tools, their perceptions of generative AI's usefulness and limitations, and what implications these perceptions hold for teaching proof-based mathematics. We conclude by discussing future considerations for integrating generative AI into proof-based mathematics instruction.