Background Despite being a priority population for HIV prevention and harm reduction programs, the sexual and reproductive health (SRH) needs of women who inject drugs are being overlooked. Furthermore, models for providing integrated SRH, HIV, and harm reduction services for women who inject drugs are rare. This article reports the development of community-based outreach services that integrated family planning and other SRH interventions with HIV and harm reduction services for this population in coastal Kenya. Methods Using mixed-methods implementation research, a qualitative baseline needs assessment was conducted with women who inject drugs and harm reduction stakeholders using a combination of in-depth interviews and focus group discussions. The qualitative data from participants was subjected to thematic analysis using Nvivo. Based on the baseline needs assessment, integration of SRH into existing HIV and harm reduction services was implemented. After two years of implementation, an evaluation of the program was conducted using a combination of qualitative interviews and review of quantitative service delivery records and other program documents. The process, impacts, and challenges of integrating SRH into a community-based HIV prevention and harm reduction program were identified. Results This article highlights: 1) low baseline utilization of family planning services among women who inject drugs, 2) improved utilization and high acceptability of outreach-based provision of SRH services including contraception among this population, 3) importance of training, capacity strengthening, technical support and financial resourcing of community-based organizations to integrate SRH into HIV prevention and harm reduction services, and 4) the value of beneficiary involvement, advocacy, and collaboration with other partners in the planning, designing and implementing of SRH interventions for women who inject drugs. Conclusions Women who inject drugs in this study had low utilization of family planning and other SRH services, which can be improved through the integration of contraceptive and other SRH interventions into existing outreach-based HIV prevention and harm reduction programs. This integration is acceptable to women who inject drugs, and is programmatically feasible. For successful integration, a rights-based beneficiary involvement, coupled with sustainable technical and financial capacity strengthening at the community level is essential. Electronic supplementary material The online version of this article (10.1186/s12978-019-0711-z) contains supplementary material, which is available to authorized users.