After the Soviet forces drove the Germans from Polish territories, NKVD general Ivan Serov invited Polish underground leaders for negotiations to discuss the aftermath of the Yalta Agreement. Pużak suspected deceit but nonetheless decided to attend to show the willingness of the resistance to work within the Yalta framework. He was promptly arrested by the Soviets, together with fifteen other Polish leaders. In the Trial of the Sixteen, which took place in Moscow in 1945, he was sentenced to 18 months in prison. Released in November 1945 after an amnesty, he refused to emigrate and instead elected to stay in Poland and continue his activity in the anti-communist opposition. During that time, he wrote his memoirs ("Wspomnienia 1939-1945", published in Paris in 1977). Pużak was again arrested by the Urząd Bezpieczeństwa in 1947 and 1948. After another show trial against leaders of the PPS-WRN, he was sentenced to 10 years in prison, which was later reduced to 5 years imprisonment. Pużak died in prison in Rawicz on April 30, 1950, and was secretly buried in Powązki Cemetery.