At the same time, Cârja took part in the resistance movement against the newly established Communist regime, and was involved in supporting the anti-communist groups in the Apuseni Mountains. Because of this and due to the political content of his writings, he spent 15 years in prison between 1949 and 1964 (in Cluj, Gherla, Aiud, and building the Danube-Black Sea Canal). He was ultimately released by a general amnesty. In parallel, his elder brother, Nicolae Cârja, was captured by the Soviet Red Army, and exiled for nine years in the Russian Far East.