After 1919 an official of the Bolshevik Party until the victory of Joseph Stalin, when he was imprisoned. He was succeeded at this post by another Bundist, Aleksandr Zolotarev. When tensions within the Bund heightened, due to the pro-Bolshevik leaning of a part of the leadership, Moisei Rafes was the leader of the centrist wing of the Bund, while Mikhail Liber and Benjamin Kheifetz led the rightists.
However, Rafes led the scissionist Kombund group in Kiev in February 1919, later joined by similar groups in Yekaterinoslav, Kharkov and Poltava, but the Kombund lasted only till May 1919, when it merged into the Ukrainian Communist Union, "Komfarband".
These moves were apparently motivated by the large-scale pogroms committed by all the armies present in Ukraine at the time, except the Red Army. After the refusal of the Soviet authorities to authorize the formation of a distinct Jewish Communist Party, Rafes, like other former Bundists Esther Frumkin, Alexander Chemerinsky and Rakhmiel Veinshtain, finally joined the upper echelons of the Yevsektsiya, the Jewish section of the Soviet Communist party (Communist Party of the Soviet Union).