As more settlers began to move into the east/central part of Natick, an area called the Needham Leg, the population shift caused a rift in the community. Those people in the more northern part of town wanted the church in the center rather than supporting the Natick Indian church in the southern part of town. This dispute continued over a period of almost sixty years. The people in the "Leg" requested the Court to restore this area of the Natick Plantation to Needham. This was approved in 1761.
The church could not be relocated without the approval of the court so the parish petitioned to become a town, and to change the name to Eliot. The name change was not granted, but Natick became a town in February of 1781. In 1796 it voted to build a new meetinghouse in the center. The inhabitants of the southern part of town did not want to support the new church and petitioned to be separated from the town. The Court resolved the issue in 1797 by restoring the "Leg" to Natick but the south and east sections remained in Needham. The Indian Church disolved as the congregation dispersed to other parishes and the building fell into disrepair. In 1828 the present Eliot Church was built, the fifth church on the site of Eliot's Meetinghouse, revitalizing the congregation and South Natick.