Intervention by the head teacher comes after a 16-year partnership between St John's primary school in Tunbridge Wells and CrossTeach.
Writing to parents, Dan Turvey said: "After careful consideration, I have decided that we will end our regular commitment to CrossTeach and that they will no longer lead assemblies or take lessons."
The school revealed concerns from parents that by welcoming workers from CrossTeach and St John's Church they exposed students to "extreme beliefs".
One unnamed parent told The Telegraph youngsters were being told "they would not go to a good place when they died" unless they believed in God.
CrossTeach said its work in schools takes place under constant supervision, and in adherence to school policies and national guidelines.
National director, Wayne Harris said the charity was "very disappointed" by the school's decision and claimed workers have never been accused of extremist views before.
He said: "Wherever possible we work in partnership with local churches and we reflect their teaching, always aiming to be sensitive to the local context, and recognising that churches vary.
"We teach mainstream Christianity."
Rev Dick Farr from St John's Church said the church completely supported Mr Turvey's letter but urged parents to remember the school was a church school.
Expressing "sadness" at his own decision, Mr Turvey added: "I do not believe CrossTeach has done anything wrong.
"They do not deserve the tarnishing of their good name and allegations of extremism that have taken place over the last few months."
CrossTeach will still be allowed to operate run a club for children and parents who decide to take part.