After the war Eustis returned to medical practice in Boston. He was once again called on to serve in military matters when Shays' Rebellion broke out in western Massachusetts in 1786, becoming surgeon to the militia force raised by General Benjamin Lincoln that quashed the rebellion in the early months of 1787. Eustis was admitted as an original member of the Society of the Cincinnati in the state of Massachusetts when it was established in 1783. He later served as Vice President of the Massachusetts Society from 1786 to 1810, and again from 1820 to 1821.