Background: The COVID-19 pandemic caused lasting disruption to healthcare systems and the mental health of frontline workers. Though the acute crisis has passed, many healthcare workers (HCWs) continue to experience long-term psychological effects, including anxiety, grief, and burnout. This mixed-methods study investigates the enduring effects of the COVID-19 pandemic on the mental health of physicians in a low-resource country. Methods: Drawing on data from the ear, nose, and throat (ENT) or otolaryngology department at a tertiary care hospital in Pakistan, the study employed an explanatory mixed-methods design, combining structured surveys and semi-structured interviews. The Hospital Anxiety and Depression Scale, the Perceived Stress Scale, and the Brief COPE Inventory were administered to 42 ENT specialists, trainees, and house officers, alongside semi-structured interviews with eight ENT physicians. Results: Survey results revealed moderate to high levels of anxiety, depression, and stress that persisted beyond the acute crisis phase of the pandemic. Interviews provided nuanced insights into the emotional burden experienced by physicians, including persistent concerns about contagion risk, professional isolation, and increased workload. Physicians described maladaptive responses and employed active coping strategies, such as seeking peer support and utilizing adaptive problem solving. Conclusions: The COVID-19 pandemic has had enduring effects on the mental well-being of physicians. Targeted interventions and policy reforms that address the ongoing pressures frontline physicians face in resource-constrained environments may help mitigate these burdens, support healthcare professionals more effectively, and improve their mental health.