Menstrual cups are gaining in popularity worldwide as a more environmentally sustainable and affordable alternative to disposable personal hygiene products. However, there is currently a lack of scientific literature regarding their safety and potential effects on women’s health. We analysed biological, demographic, and behavioural data in a cohort of young adult women using either tampons (n = 81) or menstrual cups (n = 22). We identify an increased risk of being diagnosed with fungal infection for women using menstrual cups over tampons. We did not detect significant differences between groups in terms of vaginal microbiota composition or local cytokines expression profile. However we found that depending on the type of menstrual product they use more (cups or tampons), women fall into two different clusters in a factor analysis of mixed data, which potentially reflects differences in their local vaginal environments. These results underline the urgent need for in-depth studies to better understand the potential associations between menstrual product products and women’s health.