Background It is known from previous studies that university students in sub-Saharan Africa (sSA) engage in sexual risk-taking behaviour (SRTB). However, there is paucity of data on correlates of SRTB among university students (emerging adults {EmA}) at the Kenyan Coast thus hindering intervention planning. This study seeks to provide an in-depth qualitative understanding of correlates of SRTB and their interconnectedness among university students at the Kenyan coast combining qualitative research with a systems thinking approach. Methods Using the ecological model, and employing in-depth interviews, we explored the perceptions of twenty-one EmA and five other stakeholders on what constitutes and influences SRTB among EmA at a tertiary institution of learning in Coastal Kenya. Data were analysed using a thematic framework approach. A causal loop diagram (CLD) was developed to map the interconnectedness of the correlates of SRTB. Results Our findings show that unprotected sex, transactional sex, cross-generational sex, multiple sex partnerships, gender-based violence, sex under influence of alcohol/drugs, early sex debut, and sharing sex toys were common SRTBs. Based on the ecological model and CLD, most of the reported risk factors were interconnected and operated at the individual level followed by those that operate at social level. Conclusion Our study shows that EmA are mostly engaging in unprotected sex. Enhancing sexuality education programs for students in Kenyan universities and strengthening support systems including counselling for those using alcohol/drugs may help reduce SRTB among EmA in universities in Kenya.