In healthcare workers (HCWs) and in the general population, fear of adverse effects is among the main reasons behind COVID-19 vaccine hesitancy. We present data on self-reported adverse effects from a large cohort of HCWs who underwent primary (N = 470) and booster (N = 990) mRNA vaccination against SARS-CoV-2. We described general patterns in, and predictors of self-reported adverse effect profiles. Adverse effects following immunisation (AEFI) were reported more often after the second dose of primary immunisation than after the first dose, but there was no further increase in adverse effects following the booster round. Self-reported severity of systemic adverse effects was less following booster immunisation. Prior infection with SARS-CoV-2 was found to be a significant predictor of AEFI following primary immunisation, but was no longer a predictor after booster vaccination. Compared to other studies reporting specifically on adverse effects of SARS-CoV-2 vaccination in healthcare workers, we have a relatively large cohort size, and are the first to compare adverse effects between different rounds of vaccination. Compared to studies in the general population, we have a considerably homogenous population. Insights in AEFI following primary and booster vaccinations may help in addressing vaccine hesitancy, both in HCWs and in the general population.