Like many ministers of his generation, Jeremiah Shepard encountered significant conflicts with his congregations.
Shepard found himself caught in the middle and accepted a call at the church in Lynn in 1680, where he remained for 40 years.
The Journal of Obadiah Turner described Shepard thus: "Ye new minister, Mr. Shepard, we find sound in doctrine and strong in speech; but wonderful grave and solemn, wch, after Mr. Whiting, seemeth like clouds after sunshine.
[citation needed]Turner's Journal goes on to describe Shepard's conflicts with the church at Lynn when he attempted to remove all music from the service and replace it with more preaching.
Shepard was accused of wizardry during the excitement surrounding the Salem witch trials and was vehemently opposed to the governorship of Sir Edmund Andros.