Female sex workers face existing challenges with HIV healthcare access due to structural factors (e.g., stigma, violence) and COVID-19 established further unprecedented challenges. A retrospective longitudinal design (February 2019-March 2023) was done using an interrupted time series analysis (ITS) to assess the impact of restrictions/their removal on visit numbers and Generalized Linear Models (GLM) compared patterns across the seven Sex Work Outreach Program (SWOP) clinics, with SWOP City serving as a reference clinic. The ITS analyses revealed significant variability in visit numbers across clinics and service-types due to COVID-19 restrictions. An initial decline in visits corresponded with restrictions which was followed by a rebound. HIV testing significantly dropped at some clinics, such as SWOP Majengo (estimate= -5.408, p<0.001), while ART visits remained stable. GLM analysis showed variation across clinics; for instance, condom distribution visits were significantly lower at SWOP Donholm (estimate= -0.997, p<0.001) and SWOP Langata (estimate= -0.662, p=0.022) compared to SWOP City. Findings highlight the need for adaptable health systems to sustain essential services for marginalized populations during public health emergencies. While treatment services remained stable, prevention and support services were more affected. Strengthening resilience in HIV programming requires flexible outreach strategies, adaptable clinic models, and addressing structural healthcare gaps. Possible recommendations for strengthening resilience in HIV health programming for future emergencies includes re-visiting current outreach strategies, developing flexible models and protocols that equip clinics to be accessible during future disruptions, and addressing structural gaps in healthcare to increase the engagement of female sex workers. This work also establishes a foundation for future research to be done at the patient-level to understand the specific challenges female sex workers faced when accessing these services due to the pandemic. By identifying any service gaps, this project can help support evidence-based strategies to develop inclusive and resilient public health approaches for key populations.