In later life, due to his wealth and influence as Surveyor-General, he became a patron of the new Royal Observatory at Greenwich and superintended the furnishing with astronomical instruments.

His Pendle Forest relatives were Parliamentarians but he was a Royalist. However, on 6 May 1675, 'Jonas Moore, of the Tower of London, Knight' released his half-share of Whitelee and lands adjoining Moorhiles Meadow and in Bailey Moss to Hugh Moore, which indicates that he was a copyholder of the Honor of Clitheroe. 

At a meeting of the Royal Society on 16 January 1679, Sir Jonas stated that in an area a quarter of a mile, on the top of Pendle Hill, were frequently found trees, supposed to be fir trees, buried five or six feet deep in the turf [peat] of Bailey Moss.

While travelling from Portsmouth to London he died suddenly at Godalming, Surrey on 25 August 1679 at the age of 62 and was buried in the Tower Chapel, with a salute of as many guns as he had counted years of his life.

Moore's career was fairly typical of its time but his was unusual in the use he made of his success, in the expense he lavished on his publications and his willingness to devote time, energy and money to putting the ideals he had expounded in print into practice.