Accepting a call to the church at Chebacco in 1678, Shepard encountered further opposition. The residents of Chebacco, who tired of the long trip to the church at Ipswich, Massachusetts attempted to withdraw from that church, but the members in Ipswich were unwilling that such a break be made.
In 1678, Shepard was appointed to serve at the church in Chebacco and faced further resistance. The residents of Chebacco, who grew frustrated with the distance to the Ipswich, Massachusetts church, attempted to leave that congregation but were unsuccessful as the members in Ipswich did not wish to break ties.