There is substantial evidence that contraceptive side effects are a major deterrent to consistent use of contraception but few studies in low- or middle-income countries explore the role that specific side-effects, rather than the general category of “side-effects and health concerns”, have on contraceptive dynamics. This study used population-based, longitudinal data to explore the effect that specific side-effects had on contraceptive continuation, discontinuation, and switching in Uganda. Methods Data for this study come from two rounds of PMA2020 data collection in Uganda PMA2020 Uganda’s sixth cross-sectional survey and a follow-up survey conducted one year later. The main outcomes of interest were discontinuation and switching among modern users of hormonal contraceptive methods at baseline (n=550). Multivariable multinomial logistic regressions assessed the association of reporting experiencing specific side effects (more bleeding, less bleeding, irregular bleeding, changes to sexual experience, and physical discomfort) with discontinuation and switching one year later, adjusting for socio-demographic characteristics, type of method, and length of use.Results One-third of hormonal contraceptive users reported experiencing side-effects at baseline. Reporting more bleeding increased the risk of discontinuation by 2.39 times (95% CI: 0.01-4.72). Experiencing irregular bleeding decreased the risk of switching by a factor of 0.40 (95% CI: 0.17-0.93). Changes to sexual experience or physical discomfort were both associated with increased relative risk of switching; reporting a change to sexual experience increased the relative risk of switching by a factor of 3.10 (95% CI : 0.97-9.10) and physical discomfort increased the relative risk by a factor of 1.75 (95% CI: 0.95-3.24). Wealth was significantly negatively associated with discontinuation while education was marginally significantly and positively associated with switching. Conclusions Greater attention should be paid to understanding the unique contributions of side effects to contraceptive behavior using population-based data. Not all side effects are associated with contraceptive discontinuation and switching, despite the experience of side effects being common. The experience of physical discomfort and changes to sexual experience, largely ignored in other research, were shown to affect use. Providing greater individualized care that includes information about common side effects and how they may impact daily life is necessary.