January, 1802, he was raised to the rank of major; and on the occasion of the Persian ambassador being accidentally shot at Bombay, he was again entrusted with a mission to that empire, in order to make the requisite arrangements for the renewal of the embassy, which he accomplished in a manner that afforded the highest satisfaction to the Company. In January, 1803, he was nominated to the presidency of Mysore, and to act without special instructions; and in December, 1804, he was promoted to the rank of lieutenant-colonel. In the June of the following year, he was appointed chief agent of the governor-general, and he continued to serve in that capacity until March, 1806, having successfully concluded several very important treaties during that period.
Upon the arrival in India, in April, 1808, of the new governor-general, lord Minto, colonel Malcolm was sent by his lordship to the court of Persia on a very important mission—that of endeavouring to counteract the designs of Bonaparte, then in the zenith of his power, who threatened an invasion of India by way of Persia, supported by the Persian and Turkish governments. In this difficult embassy, colonel Malcolm did not wholly succeed. He returned to Calcutta in the following August, and soon afterwards proceeded to his residence at Mysore, after having, to use the words of lord Minto, "laid the government under additional obligations to his zeal and ability." Early in the year 1810, he was again selected to proceed in a diplomatic capacity to the court of Persia, whence he returned upon the appointment of Sir Gore Ouseley, as ambassador. So favourable was the impression which he made, on this occasion, on the Persian prince, that he was presented by him with a valuable sword and star, and, at the same time, made a khan and sepahdar of the empire; to that impression, indeed, may be ascribed much of the good understanding, both in a political and commercial point of view, which afterwards subsisted between this country and Persia. During this embassy, while at Bagdad, colonel Malcolm transmitted to the government of Bengal his final report of the affairs of Persia—a document so highly appreciated, that the government acknowledged its receipt to the secret committee in terms of unqualified praise.
In 1812, colonel Malcolm again visited his native shores. He was received by the court of directors of the East India Company, with the deepest regard and acknowledgment of his merits; and shortly afterwards he received the honour of knighthood. He returned to India in 1816, and soon became engaged in extensive political and military duties; he was attached, as political agent of the governor-general, to the force under lieutenant-general Sir T. Hislop, and appointed to command the third division of the army, with which, after taking Talym by surprise, he acted a prominent part in the celebrated battle of Mehidpoor, when the army under Mulhar Rao Holkar was completely beaten, and put to rout. His skill and valour on this occasion were the theme of general admiration. A vote of thanks was awarded him, on the proposal of Mr Canning, by the house of commons; and the prince regent expressed his regret that the circumstance of his not having attained the rank of major-general prevented his creating him a knight grand cross. The intention of his royal highness to do so was, nevertheless, recorded, and in 1821 he accordingly received the highest honour which a soldier can receive from his sovereign. After the termination of the war with the Maharattas and Pindarees, to which colonel Malcolm's services had eminently contributed, he was employed by lord Hastings in visiting and settling the distracted territories of Mulhar Rao, which, and other services,, he accomplished in a most satisfactory manner, gaining to British India a large accession of territory and treasure.
At the end of the year 1821, he resolved to return once more to England; on which occasion the general orders contained the following paragraph:—
