The Mathematics for Computer Science mandatory course was conducted in a flipped classroom (FC) setting with an optional, voluntary, project-based learning (PBL) component. The objective of this study was to examine the effect of studying in an FC setting, with and without PBL, on students’ problem-solving performance, conceptual understanding, and affective perceptions. Participants were 374 undergraduate freshmen and sophomores, of whom 20% elected to participate in an optional probability PBL. The most significant finding was the reinforcement of collaboration, as reflected by teamwork on problem solving during the FC class time. The PBL students demonstrated an advantage in their performance over their peers in probability—the topic they explored, and in their positive responses regarding studying in the FC setting, with an emphasis on the collaborative learning component. The research demonstrates the importance of active engagement in a technology-based environment in which STEM undergraduate students solve problems and implement projects.