The harmonized health resource tracking implemented in Botswana and Namibia aimed to produce comprehensive data on health and HIV-related expenditure through a combined process. The approach reduced redundancies between the National Health Accounts (NHA) and National AIDS Spending Assessment (NASA) methodologies by collecting a single set of data for separate analyses. The authorities integrated CNS2011 and NASA2020 code correspondences and adapted the collection tools to obtain a level of disaggregation compatible with both methodologies. Technical skills and expert support were required to design the methodological merger, parameterize the HAPT and RTT tools and ensure the consistency of estimates, particularly for HIV non-health and capital expenditure. Capacity building, ongoing training and on-site mentoring were essential to improve data quality and the ability of assistants to administer the questionnaires. Government commitment and the buy-in of stakeholders, including international organizations and the private sector, have fostered data collection and sharing. The text emphasizes that harmonization can bring substantial efficiency gains, but requires contextual planning, the integration of code concordances into tools and the involvement of respondents. It recommends consolidated technical support, simplified tools for self-administration where appropriate, and the building of local capacity to institutionalize the tracking of health and HIV expenditure.