HIDO has a General Assembly as the highest governing body of the organization with 20 members drawn from the communities, the academia, the private sector, government and NGOs. The General Assembly meets once in a year and has major roles which include but not limited to: provide overall insight/direction about the operation of the organization, select and approve board of directors, select and approve auditors, and approve the annual report and plan of the organization.

The next governing body is the Board of Directors, which has seven members. The Board of Directors meets on a quarterly basis, and provides strategic and policy advice and guidance to the organization. HIDO has also a management committee with members including the Executive Director, Program Director, Finance and Admin Manager, and Department Heads to provide leadership and strategic direction to the day to day operation of the organization.