He was next domestic chaplain, during the latter half of 1681 and spring of 1682, to the Dowager Countess of Donegal (Letitia, daughter of Sir William Hicks) in Lincoln's Inn Fields.
Emlyn's deposition, and subsequent trial, for a blasphemous libel on the ground of an anti-trinitarian publication, did not initially involve Boyse (who had himself been under some suspicion of Pelagianism).
Next year, being absent through illness, he printed a sermon; at this synod (1723) a letter was received from him announcing a proposed change in the management of the regium donum, viz.
), in reply to William King, then chancellor of St Patrick's Cathedral, who had attacked the Presbyterians in his ‘Answer’ to the ‘Considerations’ of Peter Manby, ex-dean of Derry, who had turned Catholic.
In Emlyn's case, Boyse drew up "The Difference between Mr. E. and the Dissenting Ministers of D. truly represented", and published A Vindication of the True Deity of our Blessed Saviour, 1703 (2nd ed.
This received answers from Edward Drury and Matthew French, curates in Dublin, and the discourse itself was, without Boyse's consent, reprinted separately in 1709.
The preface to Abernethy's ‘Seasonable Advice,’ 1722, and the postscript to his ‘Defence’ of the same, 1724, are included among Boyse's collected works, though signed also by his Dublin brethren, Nathaniel Weld and Choppin.
34, 35, and the publication of the discourse, which strongly deprecated disunion threatened by the different northern and southern Presbyterian traditions, was urged by those on both sides.
Thomas Steward of Bury St Edmunds on 1 November 1726, Boyse speaks of the exclusion of the nonsubscribers as ‘the late shameful rupture,’ and gives an account of the new presbytery which the general synod, in pursuance of its separative policy, had erected for Dublin.
He published several sermons against Romanists, and a letter (with appendix) ‘Concerning the Pretended Infallibility of the Romish Church,’ addressed to a Protestant divine who had written against Rome.
Boyse wrote the Latin inscription on the original pedestal (1701) of the equestrian statue of William III in College Green, Dublin.