He later served as chaplain to the Letitia, the Presbyterian countess of Donegal, who was the daughter of Sir William Hicks, 1st Baronet.
After serving as chaplain to Sir Robert Rich, Emlyn went on to become a colleague to Joseph Boyse, a Presbyterian minister in Dublin, in 1691.
However, his tenure was cut short due to his own confession of unitarianism, and for publishing An Humble Inquiry into the Scripture Account of Jesus Christ in 1702.
In his diary, he reflects, "I thank God that He did not call me to this lot of suffering till I had arrived at maturity of judgment and firmness of resolution, arid that He did not desert me when my friends did.
Answers to Emlyn's positions were furnished by Stephen Nye (1715), Jacques Abbadie (1719), C. Alexander (1791), and Aaron Burr Sr., president of the college in New Jersey (1757),[4] on occasion of an American edition (1790) of extracts from the 'Humble Inquiry.