In 1737, the college appointed him as curate of the church in Holyhead, Anglesey, where he was a supporter of the schools of Griffith Jones, making efforts to see that the schools were regarded by the local people as Anglican rather than Methodist or Dissenting views.
He published a warning against schism in 1746, Byr Grynhoad o'r Grefydd Gristionogol, and asked John Wesley (who visited Holyhead in March 1748) to make it clear that Wesley was advising Methodists not to leave the Church.
[1] Ellis helped to promote the 1746 SPCK edition of the Welsh Bible, having earlier suggested that Richard Morris be asked to supervise its production.
He was a corresponding member of the Honourable Society of Cymmrodorion, set up by the Morris brothers.
In 1759, Jesus College appointed him to the parish of Nutfield, Surrey and his increased stipend meant that he could then afford to resign his fellowship and marry (which he did in 1762, having two children).