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The primacy of the Ologun council was disrupted by the Ogboni leaders of the many districts organizing themselves into an al-Abeokuta wide hierarchy in the pattern of the military and Ologun council. This Ogboni system, common to many Yoruba polities was derived from the city of Ile-Ife, which is said to have been the first Yoruba town in history. Its ideal function was to stand between kings and their people, preventing the former from acting as a despot and ensuring the latter did as told. It selected and controlled leaders, and preserved custom and tradition. This body was all at once the executive, legislative, and judicial body of Abeokuta.

The Parakoyi, a pre-existing Egba tradition of a "trade chiefs" union, was also developed for the whole of Abeokuta. This organization was led by the Olori-Parakoyi (head of the Parakoyi) who was in turn assisted by a number of other prominent trades people. This organization met to further common commercial interests, settle market disputes, and make regulations to ensure just prices and workmanship standards in the crafts.

All in all it has been established that Abeokuta was organized along a federal structure. The city was divided into districts which were allowed to govern themselves in whatever structure they saw fit. Above these districts existed different councils with respective domains of authority over the city at large.