Engineering education is a challenging subject due to the particularity of skills acquisition issues in nowadays context. Students need to acquire diverse talents that are essential for career prospects beyond technical skills. Project-based learning (PBL) is a submerging pedagogical approach that applies active training by targeting the different learning outcomes needed for engineers through authentic, real-world educational scenarios. Even though it offers many advantages helping students to enhance their soft skills as well as the hard ones, it also faces some challenges such as assessment mechanisms, learners engagement and motivation, teamwork and conflict management, and harmonious integration in the curriculum. In line with our commitment to excellence in engineering education, we have integrated the PBL method, harmonized it with CDIO (Conceive, Design, Implement, and Operate) standards, and combined it with a design thinking (DT) methodology. This initiative was experimented with the second-year common core computer science engineering students at ESPRIT School of Engineering. The evaluation of students in this project is based on a detailed criterion-referenced assessment (CRA) derived from the learning outcomes of the module. This competency-based evaluation includes various metrics to measure skills acquisition based on the contribution of each student, his commitment, and collaboration with the other team members, and his creative engineering skills. In this paper, we will show how effective this DT-PBL experience was thanks to the use of CRA providing detailed insight into the performance of each learner. As a consequence, we were able to collect valuable feedback to highlight the areas of improvement. Besides, this evaluation method boosted transparency by clarifying the expectations and the evaluation criteria to the learner. Based on the experiments, we will show that this valuable and meaningful competency-based educational model ensured better individual achievement in the learning process.