The COVID-19 outbreak has led worldwide governments to take preventive measures to contain the spread of the virus and its extraordinary demands upon healthcare workers. Consequently, healthcare workers have been under high pressures, putting them at risk of developing adverse outcomes. The present study aims to investigate the psychological and organizational factors that contributed to physicians’ well-being during the pandemic. A total of 78 Italian physicians participated in the study. They completed a self-report questionnaire measuring efficacy beliefs, orientation towards patient engagement, job satisfaction, non-technical skills, organizational support, sense of belonging to the hospital, job satisfaction, and mental well-being. Physicians’ sense of belonging to their hospital, efficacy beliefs about their organizations and communication with patients, as well as non-technical skills related to communication and risk awareness were positively associated with job satisfaction. In addition, the latter and sense of belonging to own hospital were positively associated with mental well-being. These findings may guide policymakers and healthcare organizations managers to consider the potential psychosocial factors related to physicians’ well-being and the required preventive measures that can help in enhancing their human and organizational resources to cope with stressful situations such as the COVID-19 pandemic.