HIDO has the General Assembly as the highest governing body of the organization with 20+ members drawn from the communities, the academia, the private sector, government and civil societies. The General Assembly meets once in a year and has major roles which include but not limited to:- providing strategic direction about the operation of the organization, select and approve board of directors, select and approve auditors, and approve the annual report and annual plan and budget 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, provides the required support to the secretariat, and provides strategic and policy advice and guidance. HIDO has also a management committee with members including the Executive Director, Program Director, Finance and Admin Director, Program Coordinators/Managers and Department Heads to provide strategic direction as well as leadership to the day to day operation of the organization.