In 1811 Pond succeeded Nevil Maskelyne as Astronomer Royal. During an administration of nearly twenty-five years, he effected a reform of practical astronomy in England comparable to that brought about by Friedrich Bessel in Germany. In 1821 he began to employ the method of observation by reflection and in 1825 devised means of combining two mural circles in the determination of the place of a single object, the one serving for direct and the other for reflected vision. Under his auspices the instrumental equipment at Greenwich was completely changed and the number of assistants increased from one to six. The superior accuracy of his determinations was attested by Seth Carlo Chandler's 1894 discussion of them in the course of his researches into the variation of latitude. Between 1810 and 1824 he persistently controverted the reality of Ireland's Astronomer Royal John Brinkley's imaginary star-parallaxes. During the 1829-31 period, he briefly served as Superintendent of the Nautical Almanac. Delicacy of health obliged his retirement in the autumn of 1835.
Among his honors were the Jerome Lalande Prize, which was conferred upon him in 1817 by the French Academy of Sciences of which he was a corresponding member, and the Copley Medal, presented in 1823. He published eight folio volumes of Greenwich Observations, translated Pierre-Simon Laplace's Système du monde and contributed thirty-one papers to scientific collections. His 1833 catalogue of positions of 1112 stars was of great value and displayed an accuracy which had previously never been achieved.
As Astronomer Royal, Pond was responsible for a substantial modernisation of the Observatory at Greenwich, extending from equipment improvements to new working practices. Perhaps his most noticeable addition was the 1833 installation of the time ball on the roof of the Observatory. Arguably, the first public time signal in the UK, the occurs daily at 1:00 p.m. and was intended to aid mariners on the Thames to synchronise their marine chronometers.
John Pond died in Blackheath, London in the year of his 69th birthday and was buried beside and near fellow Astronomers Royal Edmond Halley and Nathaniel Bliss, respectively, in the churchyard of St Margaret's in nearby Lee.