Toward the end of his life he opposed the more extreme Protestant groups, led by Anthony Ashley Cooper, 1st Earl of Shaftesbury, who refused to accept the succession of James because he was a self-declared Catholic.

[citation needed] For this reason John Robartes fought on the side of the Parliament and, according to his view of things, also the King, during the Civil War.

He always relied on his own interpretation of the Bible; annotations he made in his books show that he sympathised with those who put faith above ritual.

With the Self-Denying Ordinance of April 1645 he lost his command in Plymouth and was obliged like his brother-in-law, the Earl of Manchester, to watch the successes of Cromwell's New Model Army from the sidelines.

In 1679, for his support of Charles's policy of making his brother his successor, John was made Lord President of the Council and was created Viscount Bodmin and Earl of Radnor in the Peerage of England.

[3][5] Robartes was married twice: first to Lucy Rich, the second daughter of Robert Rich, 2nd Earl of Warwick, and Frances Hatton, with whom he had three sons, including Robert and Hender; and secondly to Letitia Isabella (died 1714), daughter of Sir John Smith of Bidborough, Kent, with whom he had nine other children, including Francis, and Araminta, who married Ezekiel Hopkins, Bishop of Derry.

Edition ornée de LXXII portraits, Graves d'apres les tableaux originaux., A Londres, [1793] (she is described by Pepys as "a great beauty indeed".)

The title of Radnor later descended to Robert's son Charles (1660–1723), who is mentioned by Jonathan Swift in his Journal to Stella, and who managed to regain the Bodvel inheritance.