Background: Limited capacity to regulate medical products is associated with circulation of products which do not meet standards of quality, safety and efficacy with negative public health and economic outcomes. This study focused on assessing the effect of the East African Community (EAC) medicines regulatory harmonization initiative on the capacity of national medicines regulatory agencies, with a focus on registration and inspection systems. Methods: An exploratory mixed-method design using both qualitative and quantitative data to access data from six national medicines regulatory authorities (NMRAs) and the EAC Secretariat. Data was collected using a combination of semi-structured interviews, questionnaires, and checklists for the period 2010/11-2015/16 with 2010/11 data serving as baseline. Heads of NMRAs, regulatory and monitoring and evaluation experts, and the EAC Secretariat Project Officer were enrolled in the study. A set of 14 indicators grouped into 6 categories were used to assess NMRAs performance. Results: Policy and legal frameworks provide a foundation for effective regulation. Collaboration, harmonization, joint dossier reviews and inspections of manufacturing sites, reliance and cooperation are key factors for building trust and capacity among NMRAs. Five out of six of the EAC Partner States have comprehensive medicines laws with autonomous NMRAs. All the NMRAs have functional registration and good manufacturing practice inspection systems supported by regional harmonised guidelines for registration, inspection, quality management and information management systems with four NMRAs attaining ISO 9001:2015 certification.Conclusions: The EAC regulatory harmonization initiative has contributed to improved capacity to regulate medical products. The indicators generated from this research can be replicated for evaluation of similar initiatives across and beyond the African continent and contribute to public health policy.