(1) Background: Medical teams are at the forefront of the COVID-19 pandemic. Decision making among medical staff is important for promoting and maintaining the health of patients and staff. This study examines factors associated with physicians’ decision making and preventive behavior during the COVID-19 pandemic in Israel. (2) Methods: An online survey was conducted among 187 Israeli physicians in April and May 2020 during the COVID-19 pandemic. The questionnaire included the levels of physicians’ perceived threat and perceived risk during the epidemic, trust in the health system, emotions, and the degree of compliance with hygiene rules and mandated behaviors. (3) Results: Most physicians reported complying with the rules of hygiene at work (73%) and full compliance with Ministry of Health guidelines (61%). The findings show that higher levels of trust, positive emotions, and threat and risk perceptions were associated with a higher degree of compliance with Ministry of Health guidelines and more careful decision making among physicians. (4) Conclusions: Levels of trust in the health system and positive emotions among healthcare staff during the pandemic are related to careful adherence to guidelines. Taking steps to maintain physical and mental health among healthcare staff is important for their functioning and for maintaining public health.