Koinonia John the Baptist is structured as a federation which unites the individual communities called Koinonia John the Baptist scattered throughout the world and which are dedicated to New Evangelization. Each Koinonia is structured into Oases/Regions and Realities made up of:

- Familial Communities: formed from members grouped together according to region. While living in their own homes, they participate in the activities and community services of their affiliated oasis. They promote Houses of Prayer which attract many brothers and sisters who are far away from faith to Christ.

- Core Families: these are families who, responding to a call from the Lord, dedicate themselves full-time to the internal work of the community and carry out specific ministries.

- Communities of Life:members who live in the same logistical area and who share everything in common within an intensely communitarian climate. These include:

- Groups of brothers and sisters who have responded to the call of the Lord Jesus to follow Him in consecrated life. They do this by taking vows of chastity, poverty and obedience;
- Family groups where members have responded to the call of the Lord Jesus to live in love sealed by the sacrament of marriage.