In its early years under Kip McKean, the ICOC operated with a highly centralized authority structure, with McKean and the Boston Church effectively holding authority over the whole movement. This structure was extensively criticized as authoritarian, leading to a crisis in 2001–2003 in which McKean resigned and the fellowship underwent significant reform.

Post-reform ICOC governance has moved toward elder-led local churches with greater autonomy, operating within a voluntary global fellowship. Individual churches are governed by elders and deacons consistent with New Testament patterns (1 Timothy 3). The global fellowship coordinates through ICOC Leadership Council meetings and regional conferences, but without the coercive centralized authority of the early years.