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Background: Despite significant investments into health improvement programmes in Uganda, health indicators and access to healthcare remain poor across the country. The PRIME trial aims to evaluate the impact of a complex intervention delivered in public health centres on health outcomes of children and management of malaria in rural Uganda. The intervention consists of four components: Health Centre Management; Fever Case Management; Patient- Centered Services; and support for supplies of malaria diagnostics and antimalarial drugs., Methods: The PROCESS study will use mixed methods to evaluate the processes, mechanisms of change, and context of the PRIME intervention by addressing five objectives. First, to develop a comprehensive logic model of the intervention, articulating the project's hypothesised pathways to trial outcomes. Second, to evaluate the implementation of the intervention, including health worker training, health centre management tools, and the supply of artemether-lumefantrine (AL) and rapid diagnostic tests (RDTs) for malaria. Third, to understand mechanisms of change of the intervention components, including testing hypotheses and interpreting realities of the intervention, including resistance, in context. Fourth, to develop a contextual record over time of factors that may have affected implementation of the intervention, mechanisms of change, and trial outcomes, including factors at population, health centre and district levels. Fifth, to capture broader expected and unexpected impacts of the intervention and trial activities among community members, health centre workers, and private providers. Methods will include intervention logic mapping, questionnaires, recorded consultations, in-depth interviews, focus group discussions, and contextual data documentation., Discussion: The findings of this PROCESS study will be interpreted alongside the PRIME trial results. This will enable a greater ability to generalise the findings of the main trial. The investigators will attempt to assess which methods are most informative in such evaluations of complex interventions in low-resource settings., Trial Registration: Clinicaltrials.gov, NCT01024426.