James Madison University faculty team-teach an interdisciplinary mathematical modeling course for mathematics and biology students. We have used two different project-based approaches to emphasize the mathematical concepts taught in class, while also exposing students to new areas of mathematics not formally covered in class. The first method allows students to select projects based on their individual interests, which provided the class with an exposure to the breadth of applications of mathematical modeling to biology. The second method allows students to select projects that are focused around one common biological theme, which encouraged a remarkable cohesion among the whole class. These strategies could be extended to various applications-based mathematics courses. We present our observations and make recommendations for project-based courses using both methods.