Both denominations shared a common Calvinistic theology, while differing in church polity (with Congregationalists and Presbyterians having adopted the Savoy Declaration and Westminster Standards respectively).
There were also many instances stretching back to colonial times where Puritan congregations embraced presbyterian polity.
[4] The Plan also made it possible for the Middle Association of Congregationalists in New York to become a subordinate jurisdiction of the Presbyterian Synod of Albany.
This ultimately led to the Old School-New School Controversy that divided the Presbyterian Church in 1837.
[7] By this time, Congregationalists had developed a greater denominational consciousness, which ultimately led to the creation of the National Council of the Congregational Churches in 1865.