Evidence exists on the health impacts of the current COVID-19 pandemic on health workers, but less is known about its impact on their work dynamics and livelihoods. This matters, as health workers—and physicians in particular—are a scarce and expensive resource in low- and middle-income countries (LMICs). Our cross-sectional survey set out to explore changes in working hours and earnings during the second year of the pandemic in a representative sample of 1183 physicians in Brazil’s São Paulo (SP) and Maranhão (MA) states. Descriptive analysis and inferential statistics were employed to explore differences in working hours and earnings among public and private sector physicians across the two locations. The workloads and earnings of doctors working exclusively in the public sector increased the most in the second year of the epidemic, particularly in MA. Conversely, the largest proportion of private-only doctors in our sample saw a decrease in their working hours (48.4%, 95% CI 41.8–55.0), whereas the largest proportion of public-only doctors in MA saw an increase in their working hours (44.4%, 95% CI 38.0–50.8). Although earnings remained broadly stable in the public sector, a third of public sector-only physicians in MA saw an increase in their earnings (95% CI 24.4–36.2). More than half of private-only doctors across both states saw a decrease in their earnings (52.2%, 95% CI 45.6–58.8). The largest proportion of dual practitioners (the majority in Brazil and in our sample) maintained their pre-pandemic levels of income (38.8%, 95% CI 35.3–42.3). As public-sector doctors have been key in the fight against the pandemic, it is critical to invest in these cadres in order to develop epidemic preparedness in LMICs, and to find new ways to harness for-profit actors to deliver social benefits.