The Iglesia Filipina Independiente has a strong tradition of authority belonging to the entire people of God. This conciliar nature of authority in the Church is expressed in the General Assembly where the clergy and laity are both represented.

The Iglesia Filipina Independiente is a Church that is governed synodically. It has the General Assembly  as the highest governing and policy-making body that regularly convenes every three years. It is consisted of all bishops, two priests in active duty, and three and three delegates representing  the  men,  women  and youth from every diocese elected in a convention, as  provided  in  Sections  1  and  2,  Article  II,  of  its Constitution.

The General Assembly operates as  a  synod  through  which  the  ordained  and  non-ordained  share  the responsibility of witnessing to the apostolic faith by virtue  of  their  common  baptism.  It  serves  as  the governing body of the Church in fulfilling the mission  entrusted  by  God,  in  safeguarding  the  unity  and continuity of the apostolic faith, and in guiding the faithful in the fulfillment of their baptismal covenant. It is thus the final authority in all matters affecting the life, order and discipline of the Church.