AMFIU’s organizational structure is both administrative and functional. In terms of administration, the Annual General Meeting (AGM) is the overall decision-making body, with an elected Board of Directors comprised of seven (7) members, responsible for overseeing the policy and strategic direction. The secretariat is headed by the Executive Director (ED), who is in charge of the day to day operations of the association.

To operationalise the structure and increase its efficiency, the human resources in AMFIU have been organized under 2 functional teams that include;

• The Management team; this is headed by the Executive Director and includes; the Manager membership and financial inclusion, the finance and administration manager (FAM), the Business Development Manager for the AMFIU Business Consult (ABC) and the information and marketing manager. This team is responsible for supervision of the day-to-day running of the organization in terms of development of workplans, supervising programme implementation, and resource mobilization and general administrative management. The team is further responsible for enhancing external relations.
• Programme Departments: To ensure efficiency 4 departments were established, namely;

• Membership and Financial Inclusion: is headed by the Manager Membership and Financial Inclusion. The focus of this team is to ensure a healthy membership development and to identify and deliver value added services to the members. It ensures that AMFIU members maintain good standards all the time, capacity building by organizing lateral learning workshops, trainings especially in areas of governance, microfinance sound practices, and consumer education among others.
• Research, Information and Marketing: is headed by the Manager Information and Marketing. Its function is to ensure strategic positioning of AMFIU as an information hub within the Ugandan microfinance industry and to collect, validate, analyze, and disseminate information from and for all industry stakeholders, primarily as an input into creating an enabling political and financial environment for the member MFIs. This department is also responsible for performance monitoring, lobby/advocacy and digital financial services.
• Finance and Administration: is headed by the Manager Finance and administration. Its function is to provide an effective back-office support system, in terms of finance and administration, for AMFIU to operate as a service provider and information hub. This is achieved through sound financial management and monitoring, logistical, and organizational support, as well as Information Communication Technology (ICT) management.
• Business Development: is headed by the Business Development Manager under the AMFIU Business Consult (ABC). AMFIU Business Consult (ABC) is the commercial wing of the Association of Microfinance Institutions of Uganda (AMFIU) established to provide fee-based products and services that promote professionalism in the microfinance sector.  The major goal of ABC is to provide quality services at affordable prices, with the ultimate goal of enhancing the provision of responsible financial services by microfinance institutions(MFIs)/SACCOs to their customers and deepening financial inclusion of all strata of the Uganda population.