When and why do citizens comply with government policies and restrictions during emergencies? We investigate possible answers to this question. We propose a mediation model where trust in government and emergency organizations as well as perceived government effectiveness mediate the relationships between participation in decision making and the willingness to comply. We also utilize the protective action decision-making model where perceptions about protective actions and threats can add to the explanation. Using a national survey distributed to a representative sample of the Israeli population during the wake of a second wave of the spread of Covid-19, we found that the willingness to comply during emergencies is related to these research variables. Participation in decision-making appears to be the main variable, but it is negatively related to the willingness to comply. We conclude that the public sector should develop and improve communication and participatory mechanisms with citizens specifically for emergencies.