Abstract Background To be in alignment with the increasing diversity in the patient population, ethnic minorities should have appropriate representation in health care professions. Medical students from ethnic minorities therefore need to be successful in their medical studies. The current literature highlights that they underperform in comparison with the ethnic majority. The aim of the present study is to gain insight into what medical students from ethnic minorities experience during their education and what they need to become or stay motivated and to perform to their full potential. Methods Medical students from ethnic minorities from year 1 to 6, enrolled at Amsterdam UMC, Faculty of Medicine, Vrije Universiteit, the Netherlands, were invited via email to participate in this study. Semi-structured interviews were conducted, using an interview guide, from August–October 2018. A constructivist paradigm was adopted. Results Eighteen medical students from ethnic minorities (three from year 1, three from year 2, one from 3, four from year 4, two from year 5, and three from year 6) participated in this study. Students’ negative experiences could be categorized as follows: (1) the effect of discrimination (2) lack of representation of ethnic minority role models, (3) lack of a sense of belonging, (4) lack of a medical network, (5) differences and difficulties in cultural communication and language, and (6) examiner bias in clinical assessments. Examples of support tips relating to these experiences are: increasing awareness about diversity and other religions, providing support groups, having visible ethnic minority role models, and facilitating support in networking. Conclusions Findings of this study suggest that medical students from ethnic minorities have negative experiences that influence their education. Supporting these students is essential for creating a good and safe educational and practical environment for ethnic minority students.