 Under the Doris Duke Charitable Foundation’s African Health Initiative, five Population Health Implementation and Training partnerships were established as long-term health system strengthening projects in five Sub-Saharan Countries. In Zambia, the Centre for Infectious Disease Research in Zambia began to implement the Better Health Outcomes through Mentorship and Assessments (BHOMA) in 2009. This was a combined community and health systems project involving 42 public facilities and their catchment populations. The impact of this intervention is reported elsewhere, but less attention has been paid to evaluation approaches that generate an understanding of the forces shaping the intervention. This paper is focused on understanding the implementation practices of the BHOMA intervention in Zambia.