Missionary work priorities of Estonian Methodist Church are:

• Missionary work abroad – missionary work outside the borders of Estonia, including missionary work among Finno-Ugric peoples;
• Inland mission – evangelical outreach in Estonia, new initiatives;
• Providing education on missionary work and evangelism – mission days, trainings, seminars; informing churches about missionary work.

EMC is currently involved in following mission projects:

• EMC has sent a missionary to Lithuania, who serves the Methodist Church there, organizes joint prayers and seminars, and visits social welfare institutions.
• Russian youth of EMC go to Nepal and help the orphanages there with repair works. This mission also helps to cover basic needs of the children in orphanages. They support building the first Christian school in Nepal and teach the children there.

There are two missionaries serving in EMC. They both work in Baltic Methodist Theological Seminary.

In cooperation with an NGO (MTÜ Damota), EMC is involved in development cooperation in Ethiopia:

• Members of EMC participate as volunteers in mission projects in Ethiopia;
• EMC congregations support children from low-income families providing them education and food;
• Members of EMC make gift packs for newborn babies in Ethiopia.

EMC supports missionary work among small nations, Khanty and Nenets, who live in Yamalo-Nenets district of Khanty land.

To support missionary work, special donations are collected, mission cafés and exhibitions are organized, and works of art are sold.