The IOM office in Accra was established in 1987. IOM Ghana is structured along the global programmatic divisions of Migration Management and Operations and Emergencies.  

Migration Management programmes in Ghana focus on Migrant Protection and Assistance (MPA), including direct assistance to vulnerable migrants, counter human trafficking, and assisted voluntary return and reintegration (AVRR); migrant health; migration policy development; migration data management; immigration and border governance (IBG); labour migration and human development; and overall capacity building on Migration Management. Operations and Emergencies programmes include managing the movements and logistics for the resettlement of refugees and supporting the Government of Ghana in preparedness and response to humanitarian emergencies. 

IOM is an active member of the UN System in Ghana, which has been working in the country since the early 1960s to support economic and social development, human rights, peace and security. The Organization works within the UN Sustainable Development Cooperation Framework (UNSDCF) 2023-2025, which presents the coherent vision and collective support of UN Agencies towards achieving Ghana’s development priorities. IOM’s activities are also aligned with and contribute to the implementation of the Coordinated Programme of Economic and Social Development Policies 2017-24. 

The Organization serves as the permanent co-chair of the UN Network on Migration (UNNM), established in 2019 together with the UN in Ghana's Resident Coordinator's Office, to facilitate effective, timely and coordinated UN system-wide support to Ghana on migration governance, including on the implementation, follow-up and review of the Global Compact for Safe, Orderly and Regular Migration (GCM). 

The IOM main office, the Canadian Visa Application Centre (CVAC) and the Migration Health Assessment Centre (MHAC) are all located in Accra. 

IOM Ghana functions under the strategic and operational guidance of the IOM Regional Office for West and Central Africa, based in Dakar, Senegal.

IOM Ghana holds the role of Country Office with Coordination Function for Togo and Benin.