He was auxiliary bishop of the Diocese of Sosnowiec from 1992 to 1998. From 1993 until 1998 he was secretary-general of the Polish bishops' conference. In 1998 he resigned his post after Piotr Libera was elected bishop and Pieronek was appointed titular bishop of Cufrura. From 1998 to 2004 he was rector of the Pontifical Academy of Theology. In 2007 he celebrated his 50th priestly anniversary with Cardinal Stanislaw Dziwisz in his residence in Kraków. In 2008, Pieronek received the Jan Karski Eagle Award to honour Pieronek's combat for tolerance and his efforts to fight against the "extremism" and alleged "antisemitic tendencies" of Radio Maryja, led by Redemptorist Father Tadeusz Rydzyk C.Ss.R. In his later years, Pieronek supported the social project of the Children's Hospice "Father Józef Tischner" in the city of Kraków. Bishop Pieronek supported the work of the Open Society Institute of George Soros.
In an interview in 2010, Pieronek claimed that Jews and the state of Israel "exploit" the Holocaust, which he labelled as such a "Jewish invention", but a crime he did not statistically or historically deny.[2] Furthermore, Pieronek stated that the suffering of people at the hands of Nazis and in concentration camps was "not exclusively Jewish", pointing to Polish prisoners and treatment of Catholic priests by Nazi authorities.[3] In the interview he said that recent Israeli and Jewish claims that Poland is antisemitic and might consider reparation payments to Jewish Holocaust survivors, were calumnious, ridiculous and a falsification of the complex history of Polish society; simultaneously Pieronek stated, that western and U.S. media and politics are dominated by Jews.[4] The Anti-Defamation League (ADL) criticized Pieronek's statement. On January 26, bishop Pieronek stated, that his statements had been taken out of context and totally misunderstood.[5]