Integrated community case management (iCCM) has now been implemented at scale globally. Literature to-date has focused primarily on the effectiveness of iCCM and the systems conditions required to sustain iCCM. In this study, we sought to explore opportunities taken and lost for strengthening health systems through successive iCCM programmes. We employed a systematic, embedded, multiple case study design for three countries—Ethiopia, Malawi and Mozambique—where Save the Children implemented iCCM programmes between 2009 and 2017. We used textual analysis to code 62 project documents on nine categories of functions of health systems using NVivo 11.0. The document review was supplemented by four key informant interviews. This study makes important contributions to the theoretical understanding of the role of projects in health systems strengthening by not only documenting evidence of systems strengthening in multi-year iCCM projects, but also emphasizing important deficiencies in systems strengthening efforts. Projects operated on a spectrum, ranging from gap-filling interventions, to support, to actual strengthening. While there were natural limits to the influence of a project on the health system, all successive projects found constructive opportunities to try to strengthen systems. Alignment with the Ministry of Health was not always static and simple, and ministries themselves have shown pluralism in their perspectives and orientations. We conclude that systems strengthening remains ‘everybody’s business’ and places demands for realism and transparency on government and the development architecture. While mid-size projects have limited decision space, there is value in better defining where systems strengthening contributions can actually be made. Furthermore, systems strengthening is not solely about macro-level changes, as operational and efficiency gains at meso and micro levels can have value to the system. Claims of ‘systems strengthening’ are, however, bounded within the quality of evaluation and learning investments.