Abstract Background Afghanistan has faced considerable challenges in healthcare delivery during the COVID-19 pandemic. These challenges were compounded by limited health literacy, shortages of skilled health workers, and fragile health infrastructure, which increased the country’s double burden of disease. The World Health Organization (WHO) recommended the use of masks as part of a comprehensive strategy to mitigate the spread of SARS-CoV-2. Nevertheless, research on mask-wearing practices in Afghanistan is limited. This study aims to investigate the factors influencing the wearing of protective gear, including masks, during the COVID-19 pandemic in Afghanistan. Methods This study analyzed 16,058 households from the 2020 Afghanistan Multi-Sector Needs Assessment (MSNA) survey data. This survey was conducted between August and September 2020 by the Racial and Ethnic Approaches to Community Health (REACH) Initiative. Sampling weighted multivariable binary logistic regression analysis was performed. Results Recent internally displaced persons (IDPs) and returnees in Afghanistan were more likely to wear protective gear to prevent COVID-19 compared to non-recent IDPs. Factors such as household sizes, household income, knowledge of humanitarian support, and the distance to healthcare facilities were significantly associated with the likelihood of wearing protective gear. Conclusions The study suggests that certain factors place crisis-affected populations in Afghanistan at high risk in COVID-19 preventive behaviors, especially in wearing protective gear. The findings in this study indicate that public health interventions should focus on improving healthcare accessibility and enhancing information dissemination while considering socioeconomic factors. Additionally, this study highlights the need for access to personal protective gear during outbreaks of infectious disease, such as the COVID-19 pandemic. Key messages • Socioeconomic factors and accessibility on health services and information can affect COVID-19 preventive behaviors in crisis-affected populations. • This study can inform public health professionals to develop adequate interventions during infectious disease outbreaks.