The European Higher Education Area (EHEA) is an opportunity to redesign medical education. Academic training is now focused on acquiring not only knowledge, but also those competencies critical to face complex professional scenarios. Together with re-evaluating traditional teaching methods, EHEA has forced a technological shift in the way we teach. By critically assessing the impact of novel teaching methodologies, we can better define biomedical education demands. Here, we address this question on a sample of medical students instructed in basic subjects along the first two academic courses. Two hundred and one medical students participated in the study (n = 128 first year, n = 73 second year). Quantitative (conventional survey statistics) and qualitative (open coding) approaches were combined to analyze data from surveys, confidential questionnaires, semi-structured interviews and open discussion. First year medical students rated more positively the use of participatory methodologies than second year students. A major drawback is detected in the perceived workload. Active teaching methodologies show a strong reliance on their time of implementation for medical students, a key aspect to be considered in the design of integrative participatory curricula along the first academic courses.