Ali failed to get an ornithologist's position which was open at the Zoological Survey of India due to the lack of a formal university degree and the post went instead to M. L. Roonwal. He was hired as guide lecturer in 1926 at the newly opened natural history section in the Prince of Wales Museum in Mumbai with a salary of Rs 350 per month. He however tired of the job after two years and took leave in 1928 to study in Germany, where he was to work under Professor Erwin Stresemann at the Berlin's Natural History Museum. Part of the work involved studying the specimens collected by J. K. Stanford in Burma. Stanford being a BNHS member had communicated with Claud Ticehurst and had suggested that he could work on his own with assistance from the BNHS. Ticehurst did not appreciate the idea of an Indian being involved in the work and resented even more, the involvement of Stresemann, a German. Ticehurst wrote letters to the BNHS suggesting that the idea of collaborating with Stresemann was an insult to Stanford. This was however not heeded by Reginald Spence and Prater who encouraged Ali to conduct the studies at Berlin with the assistance of Stresemann. Ali found Stresemann warm and helpful right from his first letters sent before even meeting him. In his autobiography, Ali calls Stresemann his "guru", to whom all his later queries went. In Berlin, Ali made acquaintance with many of the major German ornithologists of the time including Bernhard Rensch, Oskar Heinroth, Rudolf Drost and Ernst Mayr apart from meeting other Indians in Berlin including the revolutionary Chempakaraman Pillai. Ali also gained experience in bird ringing at the Heligoland Bird Observatory and in 1959 he received the assistance of Swiss ornithologist Alfred Schifferli in India.