To help prepare students to address future challenges in Science, Technology, Engineering, and Mathematics (STEM), they need to develop 21st-century skills. These skills are mediated by their beliefs about the nature of scientific knowledge and practices, or epistemological beliefs. One approach shown to support students’ development of these beliefs and skills is problem-based instruction (PBI), which encourages collaborative self-directed learning while working on open-ended problems. We used a mixed-method qualitative approach to examine how implementing PBI in a physics course taught at a Dutch university affected students’ beliefs about physics and learning physics. Analysis of the responses to the course surveys (41–74% response rates) from the first implementation indicated students appreciated opportunities for social interactions with peers and use of scientific equipment with PBI but found difficulties connecting to the Internet given the COVID-19 restrictions. The Colorado Learning Attitudes towards Science Survey (CLASS), a validated survey on epistemological beliefs about physics and learning physics, was completed by a second cohort of students in a subsequent implementation of PBI for the same course; analysis of the students’ pre- and post-responses (28% response rate) showed a slight shift towards more expert-like perspectives despite challenges (e.g., access to lab). Findings from this study may inform teachers with an interest in supporting the development of students’ epistemological beliefs about STEM and the implementation of PBI in undergraduate STEM courses.