 Jones was already a prominent citizen in Saltfleet Township. He had been a militia captain there since 1794. He also became a local magistrate. In 1801, he and his wife joined the Methodist Episcopal church in the area. Jones retired from the militia in 1811, but remained in Saltfleet Township until 1817, when he moved with his family to Brantford to live with the Mohawk community and his wife's extended family. During the War of 1812, his farm had suffered £ 250 in damages. On May 27, 1815 arsonists set fire to his barn, which Jones believed was an effort to force him to cease his investigation into a local murder of three Indians. These financial losses, coupled with prejudice from his white neighbours towards Jones due to his Indian wife and children and their knowledge he had previously been married to two Indian women simultaneously led to the move. Jones made one last survey in 1825, resurveying the line of Dundas street between Ancaster Township and West Flamborough Township. In Brantford he supported his family both by farming, and by selling of bits of land he had accumulated in his youth. After several years in Brantford, he moved to his estate Cold Springs on Dundas Street east of Paris, Ontario, where he farmed until his death.
