In religion he seems to have been tolerant by the standards of the time, causing something of a stir in 1665 when he acted as mourner at the funeral of a nonconformist clergyman. 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. These complaints were taken seriously and in 1669 and 1671 he was threatened with removal from office. He was fortunate in enjoying the friendship of the Lord Lieutenant, James, Duke of Ormonde, to whom loyalty was a cardinal virtue: as Ball remarks "those whom he ever loved, he loved to the end". Ormonde strongly defended Bysse, admitting he was slow in giving judgement but arguing that his integrity and capacity for hard work compensated for this, and he denied that there had been any fall-off in Bysse's mental abilities. These arguments were presumably successful since he was not removed from office. 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. John Bysse married Margaret Edgeworth (died 1676) daughter of Francis Edgeworth of County Longford, who held office as Clerk of the Crown and Hanaper from 1606 to c.1620. Francis was the brother and heir of Edward Edgeworth (died 1595), Bishop of Down and Connor, and ancestor of the celebrated novelist Maria Edgeworth. Margaret was the widow of John King (brother of Sir Robert King and uncle of Sir Robert King, 1st Baronet ) who was Clerk of the Crown jointly  with his father-in-law. John and Margaret had numerous children who died young, and two surviving daughters: