At the outbreak of Irish Rebellion of 1641 John Bysse, along with his younger brother Robert (who was Recorder of Drogheda, and died early in 1643) and his brother-in-law William Ball were among the leaders of the royalist and Protestant faction in Parliament.

Bysse became a substantial landowner, inheriting Preston's Inn,[4] on the site of the present City Hall, Dublin, where he built a large mansion (which was demolished in the 1760s), and also Brackenstown near Swords, which had been bought by his father around 1611.

Elrington Ball remarks flippantly that Bysse had a kind of "hereditary claim" on the Exchequer as both his father and grandfather had been officials there.

[5] In fact the author makes it clear that Bysse was eminently qualified to be Chief Baron: he had been Recorder of Dublin for 25 years and had sat in two Parliaments; he was hard-working, conscientious and popular with all political factions.

Despite Bysse's undoubted good qualities, within a few years of his appointment as Chief Baron, serious complaints were being made about his slowness and incompetence; he was even accused of senility.

In his last years, there were persistent rumours that he would either resign or be dismissed, but in fact, he remained Chief Baron until his death in 1680, aged about seventy-eight.