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Introduction: Due to the Democratic Republic of the Congo’s (DRC) precarious health system that provides only limited access to health care, the European Union, via Memisa Belgium, implemented a program to strengthen provision of and access to health care (known as PRO DS) in the provinces of Kongo Central and Ituri. This program took a holistic approach, seeking to improve equitable access and combat malnutrition. Methods: To measure the program’s social return on investment and to estimate the cost per capita and effectiveness per euro invested (efficiency), a 61-month (1 July 2017 to 31 July 2022) cost-effectiveness evaluation with a societal perspective was carried out. The double-difference method was used to compare the results of PRO DS and non-PRO DS zones. The social return on investment was assessed via the ratio of effectiveness to costs. Results: Analyses revealed the program cost between 3.72 and 3.96 euros per capita per year (2022) in Kongo Central, and between 3.12 and 3.36 euros in Ituri. Importantly, it was cost-effective in the areas of reproductive health, nutrition, and the use of health and nutrition services. Conclusions: The program’s strong nutritional component and overall holistic vision may explain why it was so efficient. PRO DS stands out from other programs that focus solely on one specific problem or population. Although the program has some limitations, it would be worthwhile for the government to invest in it.