BackgroundTo train physicians who are able to meet the evolving requirements from health care, the University of Groningen Medical Center adopted in 2014 a new curriculum named G2020. This curriculum combines thematic learning communities with competency-based medical education and Problem-based learning. In the learning community program, different learning tasks were used to train general competencies. The challenge of this program was whether students acquire similar levels of learning outcomes within the different variations of the program.MethodWe used the assessment results of three cohorts for the first two bachelor years. We used progress tests and written tests to analyze knowledge development, and the assessment results of seven competencies to analyze competence development. Concerning knowledge, we used the cumulative deviation method to compare progress tests and used the Kruskal–WallisHtest to compare written test scores between programs. Descriptive statistics are used to present all assessments of the students’ competencies.ResultsWe observed similarly high passing rates both for competency and knowledge assessments in all programs. However, we did observe some differences. The two programs that focused more on competencies development underperformed the other two programs on knowledge assessment but outperformed on competencies assessment.ConclusionThis study indicates that it is possible to train students in different learning programs within one curriculum while having similar learning outcomes. There are however some differences in obtained levels between the different programs. The new curriculum still needs to improve by balancing variations in the programs and comparability of assessments across the programs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12909-023-04341-x.