Usui's system was rooted in Tendai Buddhism and Shintoism. Tendai Buddhism (a form of mystical Buddhism) provided spiritual teachings, and Shintoism contributed methods of controlling and working with the energies. The system was based on living and practising the Mikao Usui's spiritual principles; that was the hub of the whole thing. Usui had a strong background in both kiko (energy cultivation) and a martial art with a strong Zen flavour (Yagyu Shinkage Ryu).

Usui also took Soto Zen training with Kanazawa, mentioned in the book "Crooked Cucumber" (biography of Shunryu Suzuki, a Zen Buddhist monk partly responsible for introducing Zen Buddhism to America) - Kanazawa was a close friend. Japanese people followed several paths at a time, so Usui can have been a Tendai Buddhist but followed Soto Zen for a while. 

These studies may have contributed in some way to the system that he developed, and there also seems to be a strong connection between Usui's system and Shugendo (mountain asceticism). Shugendo was a blend of pre-Buddhist folk traditions of Sangaku Shinko and Shinto, Tantric Buddhism, Chinese Yin-Yang magic and Taoism. Interestingly, Usui Sensei's precepts are his rewording of a set of precepts used in a Tendai sect of Shugendo and which can be traced back as far as the early 9th century.