His first appointment in India was as third assistant-collector and magistrate of Ratnagiri district; he was promoted to the post of second assistant in 1847, and in 1848 was made commissioner for investigating certain claims upon the Nizam's government. In 1851, Ellis arrived in Sindh as assistant-commissioner, and from 1855 to 1857 was in charge of the offices of chief commissioner during the absence in England of Sir Henry Bartle Frere. He was made special commissioner for jagirs or alienated lands in the province, before leaving Sindh in 1858. In 1859, he was collector and magistrate at Bharuch district, and, after serving as chief secretary of the Bombay government, was nominated an additional member in 1862 and an ordinary member in 1865 of the Bombay council. Five years later, he was promoted to the Viceroy's council.
Later life
In 1875, Ellis returned to England, and was made not only K.C.S.I. but a member of the Indian council in London. He took a prominent part in the affairs of the Jewish community of London, being vice-president of the Anglo-Jewish Association and of the Jews' College, where a portrait has since been placed. He published a report on education in Sindh, and edited George Stack's Dictionary of Sindhi and English. He was an active member of the Royal Asiatic Society, which he joined in 1876, and founded a prize in Bombay University; a scholarship there was established in his honour in 1875. In 1885, he retired from the Indian council, on whose deliberations he had exerted much influence. He died at Evian-les-Bains, France, on 20 June 1887, and was buried in the Jewish cemetery at Willesden, Middlesex, on 28 June. Ellis was highly regarded by his contemporaries; Sir George Birdwood described him as "one of the ablest revenue officers of the Bombay Presidency". While at Bombay, Ellis was exceptionally popular with all classes of native Indians. He was at all times accessible to them, both in India and England, and the native newspapers eulogised him unstintedly at the time of his death. He left a sum of 2,500l. in trust for the poor of Ratnajiri, his first official charge. He was not married. The Ellis Bridge in Ahmedabad, Gujarat was named after him.