This study investigated the development of perceptions of critical thinking and problem-solving skills among a group of students taking part in instructional design projects to produce digital materials using different instructional design models. The study participants were students from a computer science teaching department who were enrolled in an instructional design course. Participants were divided into two groups according to instructional design model. The rapid prototyping model (RPM) group consisted of 47 students working in 9 teams on an assignment to develop an e-book for educational use, and the Dick and Carey model (DCM) group consisted of 37 students working in 7 teams on an assignment to design digital materials to enrich courses on a specific subject. Student perceptions of the development of their critical thinking and problem-solving skills were analyzed using a causal-comparative approach, with the Big Five Personality traits as covariance. The RPM group indicated significant improvements in their perceived problem-solving skills, particularly with respect to their confidence in undertaking tasks, whereas the DCM group perceived significant improvements in their disposition to critical-thinking, particularly with respect to self-confidence and analyticity. The Openness to Experience trait was reported to be a significant covariance on the self-confidence sub-factor of both skills, as was the trait Extraversion. The findings are discussed in detail, along with recommendations for further research.