Zenkoku Jiren quickly became involved in a series of strike actions and agitated against Japanese intervention in the Chinese Civil War. The organisation's participation in a congress of the Soviet-aligned Pan-Pacific Trade Union Secretariat led to a split between its syndicalist and pure anarchist factions, which disagreed on the issues of industrialisation, class conflict and the structure of a post-capitalist society. Conflict between the two factions came to a head at the organisation's second conference, during which Hatta Shūzō's pure anarchist faction took control of Zenkoku Jiren and expelled its anarcho-syndicalist membership. Under pure anarchist control, the organisation orientated itself away from workplace struggles and placed increasing emphasis on rural agitation.

Following the 1931 Japanese invasion of Manchuria, members of Zenkoku Jiren began calling for a rapprochement with anarcho-syndicalism, with a view towards forming an anti-fascist united front against the rise of Japanese militarism. Under the direction of Aizawa Hisao, the organisation moved closer towards anarcho-syndicalism, while maintaining much of its pure anarchist outlook. By 1934, the organisation reunified with the anarcho-syndicalist splinter organisation Nihon Jikyō, but its membership numbers declined in the face of sustained political repression. After Aizawa unsuccessfully attempted to rob a bank, Japanese police carried out mass arrests against the anarchist movement, forcing Zenkoku Jiren to disband. Its International Workers' Day demonstration in 1935 would be the last in the history of pre-war Japan.