Background Kenya has made remarkable progress in integrating a range of reproductive health services with HIV/AIDS services over the past decade. This study describes a sub-set of outcomes from the Bill & Melinda Gates Foundation (BMGF)-funded Jhpiego-led Kenya Urban Reproductive Health Initiative ( Tupange ) Project (2010–2015), specifically addressing strengthening family planning (FP) integration with a range of primary care services including HIV testing and counselling, HIV care services, and maternal, newborn and child care. Methods A cross-sectional study was conducted between August and October 2013 in the cities of Mombasa, Nairobi and Kisumu in Kenya to assess the level of FP integration across six other service delivery areas (antenatal care clinic, maternity wards, postnatal care clinic, child welfare clinic, HIV testing and counseling (HTC) clinics, HIV/AIDS services in comprehensive care clinics). The variables of interest were level of integration, provider knowledge, and provider skills. Routine program monitoring data on workload was utilized for sampling, with additional data collected and analyzed from twenty health facilities selected for this study, along with client exit interviews. Descriptive analysis and Chi-square/ Fishers Exact tests were done to explore relationships between variables of interest. Results Integration of FP occurred in all the five service areas to varying degrees. Service provider FP knowledge in four service delivery areas (HTC clinic, antenatal clinic, postnatal clinic, and child welfare clinic) increased with increasing levels of integration. Forty-seven percent of the clients reported that time spent accessing FP services in the HTC clinic was reasonable. However, no FP knowledge was reported from service providers in HIV/AIDS comprehensive care clinics in all levels of integration despite observed provision of counseling and referral for FP services. Conclusions Integration of FP services in other primary care service areas including HTC clinic can be enhanced through targeted interventions at the facility. A holistic approach to address service providers’ capacity and attitudes, ensuring FP commodity security, and creating a supportive environment to accommodate service integration is necessary and recommended. Additional studies are necessary to identify ways of enhancing FP integration, particularly with HIV/AIDS care services. Electronic supplementary material The online version of this article (10.1186/s12978-019-0715-8) contains supplementary material, which is available to authorized users.

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