Objective: To describe the self-perception of basic competencies in clinical practice and evaluate their associated factors, among recently graduated physicians from Lima, Peru. Methods: Cross-sectional study. We evaluated the self-perception of the competencies in recently graduated physicians of four dimensions of the Tuning Project. Each item had six possible responses on a Likert scale: “non-existent” (1 point), “insufficient” (2 points), “sufficient” (3 points), “good” (4 points), “very good” (5 points) and “excellent” (6 points). To evaluate associated factors of the average scores for each dimension, we used linear regressions with the bootstrap method. Results: We analyzed data from 425 (54.9% were between 22 and 25 years old), which represent 31.1% of all physicians who graduated in 2016 from all medical schools located in Lima. The average self-perception score of the assessed dimensions was, in descending order: 4.49 for carrying out a patient consultation with a patient; 4.13 for carrying out practical procedures; 4.12 for providing immediate care of medical emergencies; and 4.04. for applying the principles, skills, and knowledge of evidence-based medicine (EBM). Regarding the factors associated with the average score per dimension, physicians from one university had higher average scores in all dimensions, and having done an externship and done an internship at social security hospitals was associated with a higer score with self-perception in two dimensions. Conclusion: Self-perception of competence was greater for the patient consultation dimension, and lower for the EBM. Only physicians from one university had higher average scores in all dimensions.