During World War II Petkov belonged to the National Unity Front and, following the Soviet occupation of Bulgaria in September 1944, served as minister without portfolio in the first National Unity government. He also served as general secretary of the BANU during January–July 1945. Opposed to communist domination of the government, he resigned his post to form his own political faction (BANU–Nikola Petkov) in opposition to the National Unity government.
Elected to the Bulgarian People's National Assembly in 1946, Petkov advocated policies benefiting the agricultural middle class of smallholders. Rejecting cooperation with the National Unity government, he sought the support of British and American representatives on the Allied Control Commission in Bulgaria. Stripped of his parliamentary immunity and arrested in June 1947, he was brought to trial by the government on a false charge of treason and was condemned to death on 16 August 1947. He was executed on 23 September 1947 in the Central Prison in Sofia.
Homer, John E. "The Ordeal of Nicolas Petkov and the Consolidation of Communist Rule in Bulgaria." Survey 20(1) (1974): 75–83.; Oren, Niossan. Revolution Administered: Agrarianism and Communism in Bulgaria. Baltimore: Johns Hopkins University Press, 1973.