He settled the Limerick estates on his eldest son Francis and retired to Hereford. After the Glorious Revolution of 1688, Hartstonge was anxious to resume his judicial career: he returned to Ireland and was appointed to his former office in 1691. However, despite his quarrel with the Catholic Viceroy in the previous reign, the old accusation that he was excessively tolerant of Roman Catholics was revived: he was removed from office for the second time in 1695, and retired once more to Hereford. His last years were troubled by quarrels with his eldest grandson and heir, who greatly offended him by marrying against his wishes. The turbulent career of his third wife's brother, Sir Rowland Gwynne, who was ultimately to die in a debtors' prison, was another source of worry to him. His last will is dated December 1699, and was the subject of a lawsuit in 1702. He is thought to have died in 1701. Family Hartstonge married three times. His first wife, whom he married around 1650, was Elizabeth Jermyn (or Jermy) of Gunton Hall, Norfolk, daughter of Francis Jermyn and Alice Irby, daughter of Sir Anthony Irby. They had 11 children, including Francis, Standish, John, Alice and Jane. According to the memorial stone he erected in honour of his grandfather, seven of his children, three sons and four daughters, were alive in 1676. Elizabeth died in 1663 and is commemorated by a stone plaque in St Mary's Cathedral, Limerick. His second wife was Anne Bramhall, daughter of John Bramhall, Archbishop of Armagh and Elinor Halley, who died in 1682. They had no children. His third wife was Joanna Gwynne Price, daughter of George Gwynne of Llanelwedd, Radnorshire, and his wife Sybil. Joanna was the widow of James Price and sister of Sir Rowland Gwynne, who was MP for Radnorshire, but died in a debtors' prison. She and Standish had one son, Gwynne (born 1685). His eldest son Francis died in 1688 and the title passed to Francis's son Sir Standish Hartstonge, 2nd Baronet. His son Standish followed his father to the Irish Bar and was MP for Kilkenny City from 1695 until his death in 1704. A third son John was Bishop of Ossory 1693–1714, and Bishop of Derry 1714–1717. His daughter Alice married Anthony Maude, member of the Irish House of Commons for Cashel and High Sheriff of Tipperary, and was the mother of Sir Robert