The Covenant Chain and wampum treaties are a hallmark of indigenous diplomacy and mark a critical turning point in the history of the Susquehannock. As the fur trade and conflict grew hand in hand, the instability of the region began to disrupt daily life and trade. In response, the Haudenosaunee (also known as the Iroquois confederacy) began to use their power and influence to broker peace and establish protections for smaller tribes, including the Conestoga-Susquehannock.

The Susquehannock, allied with Maryland and Virginia, entered into the covenant chain in 1677 in order to have not only peace, but also to provide security for the tribe, which was experiencing a decline in power and influence at the time. This treaty was the beginning of the diplomatic relationship between the Conestoga-Susquehannock and the Haudonosaunee confederacy to the north. This shift in power dynamics sparked a migration of Susquehannock into other territories. Some went into New York and joined the Seneca, Onondaga, and Oneida. Others moved into the territory of the Lenape and as far south as North Carolina, while others still relocated to the final centralized settlement at Conestoga.