During the Popish Plot, both John and his brother were accused of Catholic sympathies and summoned to London to account for their behaviour, but were cleared of any suspicion of disloyalty on the evidence of James Butler, 1st Duke of Ormonde, a lifelong friend of their father, and Michael Boyle, Archbishop of Armagh, who was William's father-in-law.
After the accession of James II, John is said to have opposed the King's policies and to have absented himself from Ireland for a time.
[2] Francis Elrington Ball in his History of Dublin praises John Davys as a man of prudence and integrity.
[3] By his wife, Anne Thelwall, Davys had two sons, Paul and Robert.
Under the will of their uncle Sir William Davys, whichever of them married Sir William's stepdaughter Lady Catherine MacCarty (daughter of Callaghan MacCarty, 3rd Earl of Clancarty and Lady Elizabeth Fitzgerald) would inherit the principal Davys estate, St Catherine's Park, Leixlip.