Protected areas are under immense pressure to safeguard much of the remaining global biodiversity and can be strained by unpredicted events such as the Covid-19 pandemic. Understanding the extent of the effects of the pandemic on protected area management and conservation outcomes is critical for recovery and future planning to buffer against these types of events. We used survey and focus group data to measure the perceived impact of the pandemic on protected areas in Mexico and outline the pathways that led to these conservation outcomes. Across 62 protected areas, we found substantial changes in management capacity, monitoring and tourism, and a slight increase in non-compliant activities. Our findings highlight the need to integrate short-term relief plans to support communities dependent on tourism, who were particularly vulnerable during the pandemic, and to increase access to technology and technical capacity to better sustain management activities during future crises.