IOM has been active in Malawi since when it set up an office in 2014 following the admission of  Malawi as an IOM Member  State at the IOM Member States Council in November 2013. Since then, it has contributed to the  Government of  Malawi's  (GoM) efforts to manage migration through a wide variety of projects and programs. IOM's inaugural project was to assist the government of Malawi to develop the first-ever Migration profile for Malawi in 2014. In February  2018,  IOM  signed the Cooperation Agreement with the Government of  Malawi that formalized its presence in the country through recognition as one of the Resident UN Agencies.

In Malawi, the mission has a wide range of activities, including but not limited to Assisted Voluntary Return and Reintegration (AVRR), refugee resettlement, migration and health, combating Trafficking in Persons (TiP)  and human smuggling, immigration and border management, safe migration, travel services for migrants, migration and development, emergency assistance and capacity-building on all relevant migration issues. The IOM country office is located in the Capital Lilongwe. IOM has always and continues to work within the UN Development Assistance Framework (UNDAF) whose strategic areas derive from the National Development Plan (NDP) dubbed the Malawi Growth and Development  Strategy Ill, a government framework for implementing the Sustainable Development Goals (SDGs).