University settings are socio-environmental contexts that can reduce health disparities in students with disabilities. Therefore, the aim of this study was twofold: (a) to examine the longitudinal physical activity (PA) changes of Spanish university students with disabilities during a three-year period; and (b) to identify the accomplishment of the World Health Organization's PA recommendations in this period. A three-year follow-up cohort study was conducted on 355 university students with disabilities (172 men, 183 women). The participants completed an electronic survey on PA after which a descriptive analysis, longitudinal (Wilcoxon tests) and cross-sectional pairwise comparisons (Mann-Whitney U and Kruskal-Wallis tests) were performed on non-normal data. The results show no significant PA changes during the three-year period. The cross-sectional comparisons between the waves presented a reduction in vigorous PA according to sex and similar values by age, origin of disability, and socioeconomic status. A global reduction of 0.6% was found in achieving the recommendations between the waves. We also found an increase of 5.3% in the participants classified as overweight-obese during this period. The findings offered in this study have important implications for university disability care services and sports services. University policies should focus on rethinking PA and sports programs for students with disabilities