During his first few years he fought against Hyder Ali until a definitive treaty of peace was entered into with Tippoo Sultan. In February, 1786 he was promoted to a lieutenancy. During the following years Munro was attached to military intelligence and studied the Hindustani and Persian languages, achieving a fluency not often seen among Europeans. In 1790 Tippoo Sultan broke the peace and Munro returned to active duty with the 21st Regiment. In 1796 Munro was appointed Captain and, following the siege of Seringapatam and death of Tippoo, he was given charge of the civil administration of Kanara. His success in re-establishing order and governmental control led to his promotion to Major in 1800.

He was then entrusted with the superintendence of what were called the "Ceded Districts": a certain extent of territory, yielded up in perpetuity to the British East India Company by Nizam, in lieu of a monthly subsidy which had been previously exacted from him. Munro was successful in converting one of the most disorderly provinces in India into one of the most secure and tranquil districts in the possession of the Company. During the time of his services in the Ceded Districts, Munro was promoted, 24th April, 1804, to the rank of lieutenant-colonel.

In 1807 Colonel Munro returned to England. He spent most of his time in Edinburgh, where he resumed his favourite study, chemistry, attending the lectures of Dr. Hope and reading such works on the subject as had appeared in his absence. During his residence in Britain, he took a lively interest in the Peninsular war, and was known to be in constant communication with the Duke of Wellington, who had become acquainted with him in the East. During his English hiatus he accompanied Sir John Hope to the Scheldt as a volunteer and was present at the siege of Flushing. With the East India Company's charter drawing to a close, there was a great of public inquiry into whether or not to renew it. Colonel's Munro's testimony at the various committees and inquiries led to his appointment as the head of a Special Commission with instructions to reform the judicial and police systems and he returned, now married, in 1814 to Madras, India.

In 1815 he was promoted to full colonel. While instituting civil reforms in the Madras region, in July of 1817, the Pindari War broke out with the Mabrattas and Munro asked to be re-assigned to active duty. His service was so exemplary and successful that his name became known throughout Europe and the Indian sub-continent. Canning said in the House of Commons: "He went into the field with not more than five or six hundred men, of whom a very small proportion were Europeans ... Nine forts were surrendered to him or taken by assault on his way; and at the end of a silent and scarcely observed progress he emerged ... leaving everything secure and tranquil behind him." He was promoted to Brigadier General in December of 1817. In the succeeding campaign which lasted till the beginning of August, 1818, General Munro reduced all the Peshwa’s territories between the Toombuddra and Kistna, and from the Kistna northward to Akloos on the Neemah, and eastward to the Nizam’s frontier. His health greatly impaired by the excessive fatigue which he had undergone, he resolved to resign all his commissions, both civil and military, and to retire into private life. In October of 1818 he was made a Companion of the Bath and returned with his family to England. He was however only home a few months when he received a formal communication from the government, appointing him to the governorship of Madras, and was soon after, in October 1819, promoted to the rank of major-general, and invested, November, 1819, with the insignia of K.C.B. Sir Thomas returned to India in 1820. Subsequently the Burmese war erupted, and Sir Thomas turned his attentions towards that struggle. In this war he again distinguished himself, as he had so often done before, by singular bravery, talent, and intelligence, and performed such important services that he was elevated, June 1825, to the dignity of a baronet of Great Britain. Finally in 1827, after repeated requests, Major General Sir Thomas Munro was relieved of duty and given permission to retire home to England. His replacement, the Right Honourable S. Lushington, relieved him of command in April of 1827.