The group of 16 people, which included a six-month-old baby and five other children, peacefully vacated the St. Emmeram community centre in Regensburg, Bavaria.
In a statement, the Catholic diocese of Regensburg said: "The final 16 people have left the community centre and are on their way to the authorities, who will clear up the remaining business.
"The community centre is now once again available for church use. The necessary restoration work can begin."
Church leaders initially agreed to provide shelter and food when a community, which peaked at 50 people, settled on the site at the beginning of July.
The diocese changed their approach when they stopped giving food to four remaining families, who came from various Balkan countries including Serbia and Macedonia, in a bid to remove them.
A dispute developed and involved a number of protests and a hunger strike, with members of the group reportedly claiming they would only leave the site as dead bodies.
The Bavarian Refugee Council has been quoted by a German broadcaster as saying the diocese did not help the families arrange a voluntary exit from Germany, and branded church leaders' behaviour "outrageous".
Gotthold Streitberger from the group told Deutsche Welle (DW) on Monday: "The refugees are very tense and nervous at the moment. They don't understand why they are being starved out now that they've said they want to leave."
A priest at the St. Emmeram community centre, Michael Fuchs, criticised the actions of families at the centre, telling DW: "While parents in need normally try to keep their children out of conflicts and publications, these children have been used from the beginning as banner holders, as photo objects on the protest front, and yes, in concrete threats even as potential orphans through the suicide of their parents."
Premier has approached the Bavarian Refugee Council for comment.