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Background: The COVID-19 pandemic and the associated social restrictions may have disrupted the provision of essential services, including family planning (FP) and contraceptive services. This protocol is adapted from a generic study protocol titled "Health systems analysis and evaluations of the barriers to availability and readiness of sexual and reproductive health services in COVID-19 affected areas," conducted by the World Health Organization (WHO) Department of Reproductive Health and Research., Objective: This study aims to assess the availability and use of FP and contraceptive services in primary health facilities during and after the COVID-19 pandemic; assess the risk perceptions of COVID-19 stigma, barriers to access, and quality of services from clients' and providers' perspectives in the COVID-19-affected areas; and assess the postpandemic recovery of the facilities in the provision of FP and contraceptive services., Methods: In-depth interviews will be conducted with clients-women in the reproductive age group and their male partners who visit the selected health facilities for FP and contraceptive services-and health providers (the most knowledgeable person on FP and contraceptive service provision) at the selected health facilities. Focus group discussions will be conducted with clients at the selected health facilities and in the community. The in-depth interviews and focus group discussions will help to understand clients' and health service providers' perspectives of FP and contraceptive service availability and readiness in COVID-19-affected areas. A cross-sectional health facility assessment will be conducted in all the selected health facilities to determine the health facility infrastructure's ability and readiness to provide FP and contraceptive services and to capture the trends in FP and contraceptive services available during the COVID-19 pandemic. Scientific approval for this study is obtained from the WHO Research Project Review Panel, and the WHO Ethics Review Committee has given ethical approval in the 3 countries., Results: Using a standardized research protocol will ensure that the results from this study can be compared across regions and countries. The study was funded in March 2021. It received ethics approval from the WHO Ethics Review Committee in February 2022. We completed data collection in September 2022. We plan to complete the data analysis by March 2023. We plan to publish the study results by Summer 2023., Conclusions: The findings from this study will provide a better understanding of the impact of the COVID-19 pandemic on FP and contraceptive services at the facility level, which will help policy makers and health managers develop and strengthen FP policies and services in health facilities to be more responsive to community needs., International Registered Report Identifier (irrid): DERR1-10.2196/43329., (©Rita Kabra, Beena Joshi, Ester Elisaria, Tanimola Makanjuola Akande, Komal Preet Allagh, Adesola Olumide, Deepti Tandon, Ranjan Kumar Prusty, Mary Ramesh, Donat Shamba, James Kiarie. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 10.05.2023.)