Munro held various staff appointments and served as private secretary and interpreter for successive Indian chief commanders. Throughout the Mahratta War he was closely acquainted with and in frequent contact with Colonel Arthur Wellesley, later Duke of Wellington. He also served alongside his esteemed namesake Sir Thomas Munro, 1st Baronet. John Munro helped to quell the Vellore Mutiny and was soon later appointed Quartermaster-General of the Madras Army, directly from Captain's rank, at the early age of 27.
John Munro was a leading figure in the establishment of the Travancore and Cochin states. Following the East India Company attack by Velu Thampi Dalawa, he was appointed resident of the Company in 1810 for these kingdoms. From 1812 to 1814, Col. Munro served as Diwan (Prime Minister) to the Regents Rani Gouri Lakshmi Bai and Rani Gouri Parvati Bai of Travancore and Raja Kerala Varma of Cochin. With his freedom of action, he gained the confidence of the rulers and the people in introducing the practice of having a Christian sitting on the bench next to a Brahmi in the administration of justice.
Such rulers he inspired to enact other democratic reforms. Under his tenure as Diwan, he reformed the judiciary, increased state revenue, resisted corruption and mismanagement, and began the process of abolishing slavery. On 8 March 1835 Slavery was abolished at Munroe Island and eventually by Royal decree of Travancore's maharajah in 1853 and 1855. Munro abolished many taxes imposed on the community's poorer areas.He persuaded the Rani of Travancore with strong Christian convictions to donate land in Kottayam as well as money and timber in order to establish the Orthodox Pazhaya Seminary and also asked the Church Missionary Society to send missionaries on a Aid Mission to educate and train the Malankara Church clergy. In 1816 the Church Missionary Society sent Benjamin Bailey, senior Henry Baker, and Joseph Fenn, who established what became CMS Kottayam College. The first Principal was Bailey. Bailey had the bible translated into Malayalam, with the support of Munro.Thomas Norton established a CMS School in Alleppy about the same time. The network of schools set up by missionaries, as well as their daughters, meant that Travancore led the way for both girls and boys in primary education and laid the foundations for Kerala 's high level of literacy.
John Munro had come home on leave in 1819 when his brother Hugh bought Teaninich Castle. In 1823-4 he returned briefly to India, until his retirement was forced by ill-health. He had supported the Great Disruption of 1843 as an evangelical Christian. His calotype portrait by David Octavius Hill was the model for his inclusion of the Deed of Separation at the First Assembly of the Free Church of Scotland in the famous painting by The Hill. He offered land in Alness for the Free Church, in which he was made an elder. He inherited the Teaninich distillery that the latter had established in 1817 upon Hugh 's death in 1846.On 25 January 1858 John Munro, 9th of Teaninich, died and was buried in the vault of the Teaninich family in Alness Old Parish Church.