Objectives ASSET (Health System Strengthening in sub-Saharan Africa) is a health system strengthening (HSS) programme involving eight work-packages (ie, a research study that addresses a specific need for HSS) that aims to develop solutions that support high-quality care. Here we present the protocol for the implementation science (IS) theme within ASSET (ASSET-ImplmentER) that aims to understand what HSS interventions work, for whom and how, and how IS methodologies can be adapted to improve the HSS interventions within resource-poor contexts. Settings Publicly funded health facilities in rural and urban areas in in Ethiopia, South Africa, Sierra Leone, and Zimbabwe. Participants Research staff including principal investigators, coinvestigators, field staff, PhD students, and research assistants. Interventions Work-packages use a mixed-methods effectiveness-effectiveness hybrid designs. At the end of the pre-implementation phase, a workshop is held whereby the IS theme, jointly with ASSET work-packages apply IS determinant frameworks to research findings to identify factors that influence the effectiveness of delivering evidence-informed care. Determinants are used to select a set of HSS interventions for further evaluation, where work-packages also theorise selective mechanisms. In the piloting and rolling implementation phase, work-packages pilot the HSS interventions. An iterative process then begins involving evaluation, reflection and adaptation. Throughout this phase, IS determinant frameworks are applied to monitor and identify barriers/enablers to implementation. Selective mechanisms of action are also investigated. Implementation outcomes are evaluated using qualitative and quantitative methods. The psychometric properties of outcome measures including acceptability, appropriateness and feasibility are also evaluated. In a final workshop, work-packages come together, to reflect and explore the utility of the selected IS methods and provide suggestions for future use. Structured templates are used to organise and analyse common and heterogeneous patterns across work-packages. Qualitative data are analysed using thematic analysis and quantitative data are analysed using means and proportions. Conclusions We use a novel combination of IS methods at a programmatic level to facilitate comparisons of determinants and mechanisms that influence the effectiveness of HSS interventions in achieving implementation outcomes across different contexts. The study also contributes conceptual development and clarification at the underdeveloped interface of IS, HSS and global health. The ASSET-ImplementER theme is considered minimal risk as we only interview researchers involved in the different work-packages. To this effect we have received approval from King's College London Ethics Committee for research that is considered minimal risk (Reference number: MRA-20/21-21772).