Learning-centered models, which rely on active methodologies such as Project-Based Learning (PBL), should be adopted in undergraduate programs to potentiate the development of collaboration skills within future industry professionals like civil engineers. Thus, this study reports the implementation of PBL in two successive Virtual Design and Construction (VDC) courses from an undergraduate civil engineering program: 1) VDC I, in which the VDC methodology implementation was applied theoretically in an already-built project, and 2) VDC II, in which the VDC methodology implementation was applied in a currently-under-construction project. The study's objective is to identify students' perceptions of PBL influence on their learning experience, degree of acquisition of generic competencies, and project development under the VDC methodology. To assess the PBL and VDC implementation, a survey was applied to measure students' perceptions of the three mentioned variables. Results show an increase in their perceptions about the benefits of implementing VDC and PBL for the generic competencies acquisition process by more than a third, compared to other studies which implemented Building Information Modelling (BIM) with PBL. This is due to the theoretical background of the VDC methodology in terms of collaboration, processes, and tools. Besides, VDC II students' perceptions of the generic competencies' development process, degree of learning, and project development improved by 6.13%, 7.15%, and 3.44%, respectively, compared to VDC I students' perceptions, which is owed to the natural interaction between students and stakeholders of the projects adopted.