Research in the past decades has repeatedly revealed that first year university students struggle to understand two-dimensional projectile motion concepts. In contrast to high school, projectile motion frequently makes use of components and it requires at least a basic understanding of trigonometry concepts. To follow the lessons and generate conceptual understanding in two-dimensional projectile motion, students need to connect the concepts developed in the last three years of high school. The present study compared the effects of two instructional approaches, i.e. projectile motion Physics Education Technology (PhET) simulation vs. phenomenon-based experiential learning, on students’ conceptual understanding of the integration of motion along two independent axes among first-year physics students. A purposive sample consisted of 154 first-year physics students at a public university in South Africa. The study adopted an experimental, mixed-method research design. A self-developed and piloted Projectile Motion Conceptual Test and semi-structured interviews with 12 students from across the performance spectrum were used for data collection. A reliability coefficient of 0.72 was established using the Kuderson–Richardson correlation moment coefficient. The results denoted that PhET simulation outperformed phenomenon-based experiential learning in improving students’ conceptual understanding of the integration of motion along independent axes in projectile motion. The ANOVA-test showed that the PhET groups achieved significantly higher scores on the post-test than phenomenon-based experiential learning groups. The findings of this study are diagnostic and they assist module designers in determining conceptual difficulties students face in projectile motion.