Skills assessment is a topic within experiential learning teaching pedagogy, such as challenge-based learning (CBL), which calls for attention. Most university teachers know how to assess and judge the knowledge levels of their engineering students but need to learn more about assessing the so-called 21st-century skills (e.g., leadership, problem-solving, empathy, communication) and how the assessment influences the learning process. Therefore, this paper aims to study the connections between the learning process and skills assessment in innovation and entrepreneurship education (I&E) initiatives and discuss how to assess student’s skills in a transparent and safe way. To achieve that scope, we compare and critically discuss four I&E education experiences from the University of Trento (Italy) and Linköping University (Sweden), considering different variables such as learning goals, contents, team formation, teamwork, and expected outcomes. We identify four main findings: (i) facilitation and coaching are an essential ingredient in the courses, (ii) development-oriented feedback from teachers helps students to acquire new knowledge and improve their skills, (iii) formative assessment - both informal and formal - through matrices can help teachers in measuring progressions and difficulties in individual students, (iv) ENTRECOMP framework can support the soft skills evaluation. In conclusion, we underline the importance of assessing skills on two levels (the individual and the team) through recognized and well-described tools. Secondly, personalized self-directed learning tools, such as structured learning reflection and tailor-made learning criteria, are also beneficial but have limitations. Finally, formative assessment matrices, with defined requirements for different levels, also seem helpful.