Integrating methadone and HIV care is a priority in many low- and middle-income settings experiencing a growing challenge of HIV epidemics linked to injecting drug use. There is as yet little understanding of how to integrate methadone and HIV care in these settings and how such services can be implemented; such a gap reflects, in part, limitations in theorizing an implementation science of integrated care. In response, we qualitatively explored the delivery of methadone after its introduction in Kenya to understand integration with HIV care. Semi-structured interviews with people using methadone (n = 30) were supplemented by stakeholder interviews (n = 2) and participant observation in one city. Thematic analysis was used, that also drew on Mol’s logic of care as an analytical framework. Respondents described methadone clinic-based care embedded in community support systems. Daily observed clinic care was challenging for methadone and stigmatizing for HIV treatment. In response to these challenges, integration evolved and HIV care differentiated to other sites. The resulting care system was acceptable to respondents and allowed for choice over locations and approaches to HIV care. Using Mol’s logic of care as an analytical framework, we explore what led to this differentiation in integrated care. We explore co-production and experimentation around HIV care that compares with more limited experimentation for methadone. This experimentation is bounded by available discourses and materials. The study supports continued integration of services whilst allowing for differentiation of these models to adapt to client preferences. Co-location of integrated services must prioritize clinic organization that prevents HIV status disclosure. Our analysis fosters a material perspective for theory of implementation science and integration of services that focuses attention on local experimentation shaped by context.