Member Denominations:  These form highest organ of the Alliance, the Annual General meeting. While the role of the Alliance will be facilitative, members will carry out activities at denominational and congregational levels. The Alliance provides oversight and linkages for networking at a national level. The members have ultimate responsibility for good governance and prudent management of resources.

Para-Church Organizations: The Alliance recognizes that collaboration with evangelical Para-church organizations creates the synergy needed to effectively address some of the issues affecting the evangelicals. The Alliance forges partnerships and Alliances with likeminded national and international mission agencies/organizations that add value to her work. EAK works in close collaboration with; Fellowship of Christian Unions (FOCUS), Emerging Young Leaders (EYL), Finish The Task (FTT), Trans-World Radio (TWR), FEBA Radio, Life Challenge Africa, Church Mission Society (CMS), Compassion International, Life Ministry and World Vision International.

WEA and AEA: The Alliance is an active member of the World Evangelical (WEA) Alliance and the Association of Evangelicals in Africa (AEA). Supporting Partners: Evangelical Alliance of Kenya has since 2002 been in partnership with several agencies. Among these is Tearfund UK. Tearfund UK has been instrumental in the revival and has facilitated the organizational development process for EAK. Inter Religious Council of Kenya (IRCK) has been supporting HIV and AIDS interventions to EAK member churches.

Government Agencies: The Alliance works closely with a number of government agencies to address some of the strategic areas of focus. These include National Campaign Against Drug and Substance Abuse (NACADA), National Anti-Corruption Commission (NACC), Kenya Anti-Corruption Authority (KACC) and law enforcement agencies, the Multi-Sectoral Constitution Review Council (MSCRC), the police and judiciary.

Development Agencies: The Alliance recognizes that development agencies play a crucial role in development in Kenya, particularly in community development. The Alliance has identified like-minded agencies that it works closely with. These include NGOs, CBOs, and UN Agencies that are involved in socio-economic development either at community or national levels. It also seeks support of international agencies to support initiatives aimed at promoting socio-economic development particularly of the marginalized groups and areas in Kenya.