Menstrual problems affect many young women worldwide, conditioning both their academic performance and quality of life. This study sought to analyse the prevalence of menstrual problems and their possible relationship with lifestyle among Spanish university women, as part of a research project (UniHcos Project) involving a cohort of 11 Spanish universities with 7208 university students. A descriptive analysis was performed using the bivariate chi-square test and the Student’s t-test together with a binary logistic regression, in which the dependent variable was ‘suffering from menstrual problems’. Menstrual problems were identified in 23.8% of the students, representing women who paid more visits to the doctor and to emergency rooms, and who consumed more painkillers and contraceptives. In relation to dietary preferences, menstrual problems were 1.39 (CI 95% 1.22–1.61; p = 0.000) times more likely among women classified as high-risk alcohol users according to the AUDIT questionnaire, and 1.187 (CI 95% 1.029–1.370; p = 0.019) times greater among those who consumed sweets daily, 1.592 (CI 95% 1.113–2.276; p = 0.011) times more frequent among those who eat fish daily, and 1.199 (CI 95% 1.004–1.432; p = 0.045) times greater among those who were dieting. Menstrual problems affect many college students and potentially modifiable lifestyle variables exist which may influence their prevalence. It would be interesting to develop programmes to promote women’s health in the university context.