This study is based on the constructivist theory approach, employing a qualitative methodology in the form of an instrumental case study. Semi-structured interviews were conducted with 15 teachers in two hospitals in Bogotá during October and November 2024. These interviews explored their perceptions of Evidence-Based Medicine (EBM) and the methods they use to teach its principles in a clinical setting. Through thematic analysis, the main pedagogical approaches and challenges faced by teachers in teaching EBM were identified. The results highlight four key themes. First, teaching strategies rely on clinical rounds, journal clubs, and case analyses, with a strong emphasis on the critical appraisal of the literature. Second, teachers emphasize the importance of integrating scientific evidence into clinical practice, including thorough literature searches and analysis to support decision-making. Third, they recognize clinical experience as an essential complement to EBM but find it challenging to teach how to balance evidence and clinical judgment in complex scenarios. Fourth, while the integration of patient preferences is considered crucial, it often boils down to explaining medical conduct rather than fostering truly shared decision-making that reflects the patient’s values and expectations. Conclusions: The conclusions indicate that EBM teaching focuses predominantly on scientific evidence, while integrating patient preferences and clinical experience is regarded as indirect or secondary. Teachers interpret considering patient preferences as explaining their health status rather than truly including their values or psycho-emotional factors in decision-making. Additionally, they perceive the teaching of clinical experience as something residents learn indirectly by observing their instructors, rather than through explicit instruction on balancing clinical judgment and scientific evidence. This limited approach could constrain a comprehensive understanding of EBM, leaving residents inadequately prepared to address the complexities of healthcare. To enhance EBM teaching and train physicians capable of providing comprehensive care, it is essential to adapt the curriculum to explicitly include empathetic communication skills and shared decision-making, ensuring that future physicians can appropriately combine scientific evidence with the individual needs and values of their patients.