In a statement Mars Hill said it had taken the decision because it was "seeking to operate within our current means."
Buildings in Seattle, Phoenix and Huntington Beach will close with some being merged with nearby churches.
"If you attend one of these churches, we are deeply sorry," the statement said.
It added: "I also want you to know we take this very seriously, your pastors grieve over this, and we have made these decisions with great care, and after much prayer."
Mars Hill has been under the spotlight since founding member Mark Driscoll decided to take a six week break from preaching whilst allegations against him were investigated.
It's thought negative coverage in the media has led to financial troubles for the church which has grown rapidly.
At the start of 2014 attendance was around 12 to 13 thousand but since controversy surrounding Mr Driscoll emerged it's fallen to around nine thousand.
At the start of the month a number of elders and staff members resigned from the Church with the organisation saying it expected more people to follow.
A spokesperson said: "As we have shared before, we have taken the concerns and disagreements submitted to us seriously, and our Board of Elders is reviewing the content of the letters we have received."