Background: Medical education has a longstanding tradition of using logbooks to record activities. The portfolio is an alternative tool to document competence and promote reflective practice. This study assessed the acceptance of portfolio use among Saudi undergraduate medical students. Methods: Portfolios were introduced in the 2nd through 5th years at King Abdulaziz University over a two-year period (2013–2015). At the end of each academic year, students completed a mixed questionnaire that included a self-assessment of skills learned through the use of portfolio. Results: The results showed a difference in focus between basic and clinical years: in basic years students’ focus was on acquiring practical skills, but in clinical years they focused more on acquiring complex skills, including identifying and managing problems. The questionnaire responses nonetheless revealed a positive trend in acceptance (belief in the educational value) of portfolios among students and their mentors, across the years of the program. Conclusions: Using portfolios as a developmental learning and formative assessment tool in the early undergraduate years was found to contribute to students’ ability to create their own clinical skills guidelines in later years, as well as to engage in and appreciate reflective learning.