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Abstract Background Competency-based education has been considered the most important pedagogical trend in Medicine in the last two decades. In clinical contexts, competencies are implemented through Entrustable Professional Activities (EPAs) which are observable and measurable. The aim of this paper is to describe the methodology used in the design of educational tools to assess students´ competencies in clinical practice during their undergraduate internship (UI). In this paper, we present the construction of specific APROCs (Actividades Profesionales Confiables) in Surgery (S), Gynecology and Obstetrics (GO) and Family Medicine (FM) rotations with three levels of performance. Methods The study considered a mixed method exploratory type design, a qualitative phase followed by a quantitative validation exercise. In the first stage data was obtained from three rotations (FM, GO and S) through focus groups about real and expected activities of medical interns. Triangulation with other sources was made to construct benchmarks. In the second stage, narrative descriptions with the three levels were validated by professors who teach the different subjects using the Delphi technique. Results The results may be described both curricular and methodological wise. From the curricular point of view, APROCs were identified in three UI rotations within clinical contexts in Mexico City, benchmarks were developed by levels and validated by experts’ consensus. In regard to methodological issues, this research contributed to the development of a strategy, following six steps, to build APROCs using mixed methods. Conclusions Developing benchmarks provides a regular and standardized language that helps to evaluate student’s performance and define educational strategies efficiently and accurately. The university academic program was aligned with APROCs in clinical contexts to assure the acquisition of competencies by students.