The General Assembly, the highest body of BIOFUND, meets annually to approve the plans and activity reports of the Foundation and to elect the members of the Board of Directors and of the Supervisory Board. The Assembly consists of relevant figures, both Mozambican and foreign, from the public sector, the private sector, civil society, academic institutions and also representatives of the donors.

BIOFUND is managed by a Board of Directors of 7-9 members, from the various sectors represented in the General Assembly (Government, NGOs, Financial Management, Academia, Civil Society, Donors), which is responsible for the organisation, implements the strategic plan and the annual plans, defines general guidelines, and approves the investment policy and the plan of subventions to be granted.

The Board of Directors sets up consultative bodies and working committees for various purposes. Among these there stands out the Investment Committee, which supervises the financial applications of the Foundation made by professional asset managers.
To handle the day-to-day affairs of the Foundation, the Board of Directors delegates the necessary powers to the Executive Director. The Executive leadership also includes a Director of Administration and Finance, a Programs Director and Director of Innovative Financing.

The Supervisory Board, composed of three members, is responsible for inspecting annually all the administrative and financial activities of BIOFUND, including its accounts and reports, and for drawing up an opinion on activities that result in an increase or reduction of income.