Background: Coronavirus disease (COVID-19) vaccine-related side effects have a determinant role in the public decision regarding vaccination. Therefore, this study has been designed to actively monitor the safety and effectiveness of COVID-19 vaccines globally. Methods: A multi-country, three-phase study including a cross-sectional survey to test for the short-term side effects of COVID-19 vaccines among target population groups. In the second phase, we will monitor the booster doses’ side effects, while in the third phase, the long-term safety and effectiveness will be investigated. A validated, self-administered questionnaire will be used to collect data from the target population; Results: The study protocol has been registered at ClinicalTrials.gov, with the identifier NCT04834869. Conclusions: CoVaST is the first independent study aiming to monitor the side effects of COVID-19 vaccines following booster doses, and the long-term safety and effectiveness of said vaccines.