Siddiqui was the first scientist to bring the anthelmintic, antifungal, antibacterial, and antiviral constituents of the Neem tree to the attention of natural products chemists. In 1942, he extracted three bitter compounds from neem oil, which he named as nimbin, nimbinin, and nimbidin respectively. The process involved extracting the water-insoluble components with ether, petrol ether, ethyl acetate and dilute alcohol. The provisional naming was nimbin (sulphur-free crystalline product with melting point at 205 °C, empirical composition CHO), nimbinin (with similar principle, melting at 192 °C), and nimbidin (cream-coloured containing amorphous sulphur, melting at 90–100 °C). Siddiqui identified nimbidin as the main active antibacterial ingredient, and the highest yielding bitter component in the neem oil. These compounds are stable and found in substantial quantities in the Neem. They also serve as natural insecticides.
In acknowledgement of these revolutionary discoveries, he was awarded the Order of the British Empire in 1946.
In his later career, Siddiqui continued to discover and isolate numerous unique anti-bacterial compounds from various parts (leaves, bark, etc.) of the Neem and other plants. He had more than 50 chemical compounds patented in his name in addition to those discovered as a result of his joint research with other colleagues and students. Most of these discoveries still remain vital natural ingredients of various medicines as well as biopesticides.