Goren's career was characterized by a commitment to the Religious Zionist values of his youth. He volunteered for the Haganah in 1936, and served as a chaplain for the Jerusalem area during the 1948 War of Independence, during which he tested for and qualified as an IDF paratrooper. Goren was a Chaplain of the Carmeli Brigade during the war. Immediately after the War of Independence, he engaged, often at great personal risk, in the collecting of the bodies and giving proper burial to soldiers whose remains had been left in the field. He strongly opposed the idea of separate religious and secular units and worked for the integration of all soldiers in united army units. He was the most prominent halakhist involved in rulings for religious soldiers regarding their army service. Goren was eventually promoted to the rank of Brigadier-General.