The movement that caused the churches in the colony to split into factions was the Great Awakening movement.
The movement consisted of basically of preachers that altered messages and reemphasizing concepts of Calvinism. They changed thoughts that humans were sinners from their birth and God was an angry judge to thoughts that God was a good person that would forgive humans in case of sins and that humans were responsible for their own happiness.
This caused new denominations of Church to come up, such as Methodists, Baptists and, Presbyterians.