INTRODUCTION: The South African Department of Health has developed and implemented the Integrated Chronic Disease Management (ICDM) model to respond to the increased utilisation of primary healthcare services due to a surge of non-communicable diseases coexisting with a high prevalence of communicable diseases. However, some of the expected outcomes on implementing the ICDM model have not been achieved. The aims of this study are to assess if the observed suboptimal outcomes of the ICDM model implementation are due to lack of fidelity to the ICDM model, to examine the contextual factors associated with the implementation fidelity and to calculate implementation costs. METHODS AND ANALYSIS: A process evaluation, mixed methods study in 16 pilot clinics from two health districts to assess the degree of fidelity to four major components of the ICDM model. Activity scores will be summed per component and overall fidelity score will be calculated by summing the various component scores and compared between components, facilities and districts. The association between contextual factors and the degree of fidelity will be asseseed by multivariate analysis, individual and team characteristics, facility features and organisational culture indicators will be included in the regression. Health system financial and economic costs of implementing the four components of the ICDM model will be calculated using an ingredient approach. The unit of implementation costs will be by activity of each of the major components of the ICDM model. Sensitivity analysis will be carried out using clinic size, degree of fidelity and different inflation situations. ETHICS AND DISSEMINATION: The protocol has been approved by the University of Cape Town and University of the Witwatersrand Human Research ethics committees. The results of the study will be shared with the Department of Health, participating health facilities and through scientific publications and conference presentations.