Purpose: The purpose of the study is to determine when students deepen their conceptual understanding of mathematical modeling during a one-semester course in biomedical engineering that uses the constructivist problem-based learning (PBL) framework. The study hypothesizes that concept maps, as a form of assessment, would show increased complexity and quality after the completion of PBL projects. Methods: Students generated concept maps addressing their understanding of biomedical engineering mathematical modeling at multiple time points in the semester before and after the completion of two team-based PBL projects. The concept maps were quantitatively evaluated to determine their complexity as well as holistically evaluated to determine their quality. The quantitative and qualitative metrics were statistically evaluated across collection time points. Results: The analysis demonstrates significant increases in concept map complexity and quality between the beginning and end of the semester. In contrast, there were no significant increases following a 3-week instructor-guided PBL activity. These results indicate that students need to complete their own project to demonstrate a deeper understanding of mathematical modeling. Conclusions: These findings highlight concept maps as valuable tools for tracking conceptual learning in biomedical engineering education and suggest PBL as an effective teaching method for developing integrated knowledge.