Objectives: Medical nutrition education aims to equip doctors with nutrition knowledge, skills, attitudes and confidence to counsel patients to improve their diet. This study aimed to describe changes in medical students’ self-perceived nutrition competence at three time points during medical training. Design: Prospective longitudinal observational study. Setting: The University of Auckland, School of Medicine. Participants: Year 2 medical students (phase 1, preclinical) were surveyed in May 2016. Participants repeated the survey in February 2018 as Year 4 students and July 2019 (phase 2, clinical) as Year 5 students. Primary outcome measure: Primary outcome measure was self-perceived nutrition competence measured using the validated NUTrition Competence (NUTCOMP) survey. Results: In 2016, 102 of 279 eligible Year 2 medical students completed the survey (response rate (RR 36.7%)). In 2018, 89 Year 4 students repeated the survey (RR 87.3%) and 30 students as Year 5 students in 2019 (RR 29.41%). There was a significant increase in total NUTCOMP scores (knowledge, skills, confidence to counsel and attitude towards nutrition) between Year 2 and Year 4 (p=0.012). There was a significant increase in the confidence to counsel construct (mean difference 7.615, 95% CI 2.291 to 12.939, p=0.003) between Year 2 and Year 4. Constructs with lowest scores at all time points were nutrition knowledge and nutrition skills. There was clear desire for more nutrition education from all students: Year 2 (mean=3.8 out of 5 (1.1)), Year 4 (mean=3.9 out of 5 (0.9)), Year 5 (mean=3.8 out of 5 (0.8)). Conclusion: Medical students’ self-perceived nutrition competence in providing nutrition care increased modestly at three points throughout medical training. There remains opportunity for further supporting medical students to increase their competence in nutrition care, which could be achieved through mandatory and greater medical nutrition education.