On his return to India in 1930, he discovered that the guide lecturer position had been eliminated due to lack of funds. Unable to find a suitable job, Salim Ali and Tehmina moved to Kihim, a coastal village near Mumbai. Here he had the opportunity to study at close hand, the breeding of the baya weaver and discovered their mating system of sequential polygamy. Later commentators have suggested that this study was in the tradition of the Mughal naturalists that Salim Ali admired and wrote about in three part series on the Moghul emperors as naturalists. A few months were then spent in Kotagiri where he had been invited by K M Anantan, a retired army doctor who had served in Mesopotamia during World War I. He also came in contact with Mrs Kinloch, widow of BNHS member Angus Kinloch who lived at Donnington near Longwood Shola, and later her son-in-law R C Morris, who lived in the Biligirirangan Hills. Around the same time he discovered an opportunity to conduct systematic bird surveys in the princely states of Hyderabad, Cochin, Travancore, Gwalior, Indore and Bhopal with the sponsorship of their rulers. He was aided and supported in these surveys by Hugh Whistler who had surveyed many parts of India and had kept very careful notes. Whistler published a note on The study of Indian birds in 1929 where he mentioned that the racquets at the end of the long tail feathers of the greater racket-tailed drongo lacked webbing on the inner vane. Salim Ali wrote a response pointing out that this was in error and that such inaccuracies had been carried on from early literature and pointed out that it was incorrect observation that did not take into account a twist in the rachis. Whistler was initially resentful of an unknown Indian finding fault and wrote "snooty" letters to the editors of the journal S H Prater and Sir Reginald Spence. Subsequently, Whistler re-examined his specimens and not only admitted his error but became a close friend. Whistler wrote to Ali on 24 October 1938:
Salim Ali wrote numerous journal articles, chiefly in the Journal of the Bombay Natural History Society. He also wrote a number of popular and academic books, many of which remain in print. Ali credited Tehmina, who had studied in England, for helping improve his English prose. Some of his literary pieces were used in a collection of English writing. A popular article that he wrote in 1930 Stopping by the woods on a Sunday morning was reprinted in The Indian Express on his birthday in 1984. His most popular work was The Book of Indian Birds, written in the style of Whistler's Popular Handbook of Birds, first published in 1941 and subsequently translated into several languages with numerous later editions. The first ten editions sold more than forty-six thousand copies. The first edition was reviewed by Ernst Mayr in 1943, who commended it while noting that the illustrations were not to the standard of American bird-books. His magnum opus was however the 10 volume Handbook of the Birds of India and Pakistan written with Dillon Ripley and often referred to as "the handbook". This work began in 1964 and ended in 1974 with a second edition completed after his death by others, notably J S Serrao of the BNHS, Bruce Beehler, Michel Desfayes and Pamela Rasmussen. A single volume compact edition of the Handbook was also produced and a supplementary illustrative work, the first to cover all the birds of India, A Pictorial Guide to the Birds of the Indian Subcontinent, by John Henry Dick and Dillon Ripley was published in 1983. The plates from this work were incorporated in the second edition of the Handbook. He also produced a number of regional field guides, including The Birds of Kerala (the first edition in 1953 was titled The Birds of Travancore and Cochin), The Birds of Sikkim, The Birds of Kutch (later as The Birds of Gujarat), Indian Hill Birds and Birds of the Eastern Himalayas. Several low-cost book were produced by the National Book Trust including Common Birds (1967) coauthored with his niece Laeeq Futehally which was reprinted in several editions with translations into Hindi and other languages. In 1985 he wrote his autobiography The Fall of a Sparrow. Ali provided his own vision for the Bombay Natural History Society, noting the importance of conservation action. In the 1986 issue of the Journal of the BNHS he noted the role that the BNHS had played, the changing interests from hunting to conservation captured in 64 volumes that were preserved in microfiche copies, and the zenith that he claimed it had reached under the exceptional editorship of S H Prater.