R. Sonnenfeld stood for complete separation between the Orthodox and the non-Orthodox; he strongly opposed the bringing of the institutions of the old yishuv under the control of the Zionist bodies and the participation of the Orthodox in the official community, Keneset Yisrael, and fought for the statutory right of every individual to opt out of it. As a result of his adherence to the doctrine of separation, R. Sonnenfeld was one of the chief opponents of R. A. I. Kook, and led the opposition to his appointment as rabbi of Jerusalem, and later as chief rabbi of Erez Israel, even though on the personal level their relationship was one of friendship and esteem. In 1920 R. Sonnenfeld was elected rabbi of a separate Orthodox community.