Despite being a burgeoning research topic, well-being is still a neglected issue to a large degree in Indonesia. In educational context, well-being may play an important part in students’ resilience, achievements, and future flourishing in life. Moreover, while there have been rapid changes in the landscape of Indonesian medical education, there is an assumption that those who succeeded in entering medical school were amongst the most talented, competent, and capable component of the society, and as such more impervious to well-being issues. A paucity in the literature concerning the well-being of the medical student population in Indonesia was identified. The purpose of the study was to gain an understanding of the well-being of medical students with a focus on the students themselves. Specifically, the well-being of Indonesian medical students is explored using semi-structured interviews of 46 third and fourth-year undergraduate students in 10 Indonesian medical schools, acquired by means of purposive and snowball sampling methods. After Giorgian descriptive phenomenological analysis of the data, an essence of what being well is for the students emerged: it is being fulfilled, empowered, and grateful. The students acquired a sense of flourishing as a person throughout medical school, and their resilience developed along the way. There are many contributors that influence both the students’ well-being and resilience. Resilience-related issues were interestingly pronounced when participants discussed negative aspects of their lives and were closely related to sense of deficiency. Echoing scholars’ concern, mention of systematic intervention from the schools in developing and maintaining students’ well-being and resilience was scarce. Overall, the findings helped rectifying the Euro-American bias in the literature regarding the topic, while to some extent agreeing with previous studies. Further recommendations are presented.