The parishes of the Diocese of the Midwest are organized into administrative deaneries based on geographic location. The diocese has six deaneries, each deanery has a Dean elected by the Archbishop's Council (all six deans and the chancellor) and confirmed by the Archbishop. The work of the deanery is overseen and guided by the Dean who is a parish priest from within the respective deanery.

He coordinates and directs activities of the parishes and priests within the deanery, guiding the establishment of missions, and serving as the first appeal if or when disputes arise within the deanery.

In all things, the Deans report directly to the Archbishop, from whom they receive advice, instruction, and counsel, and for whom they act as an administrative liaisons to their own deanery communities.