Penderecki has twice received the Prix Italia - in 1968 for his Dies irae Oratorium ob memoriam in perniciei castris in Oswiecim necatorum inexstinguibilem reddendam for three solo voices, mixed choir and orchestra (1967), and in 1972 for his work, Passio et mors Domini Nostri Jesu Christi secundum Lucam for three solo voices, speaker, three mixed choirs, boys' choir and orchestra (1963-66). In addition, Penderecki has received the following awards: the first state prize (1968, 1983); the award of the Polish Composers' Union (1970); the Gottfried von Herder Award from the W.v.s. Foundation in Hamburg (1977); the Jean Sibelius Award from the Wilhouri Foundation in Helsinki (1983); Premio Lorenzo Magnifico, Florence (1985); the award of the Karl Wolff Foundation (Israel, 1987); a Grammy Award from the National Academy of Recording Arts and Sciences (USA) for his Cello Concerto No. 2, with Mstislav Rostropovich (1988); the Grawemeyer Award of the University of Louisville (1992); the award of the UNESCO International Music Council (1993), Order for Merits for Monaco (1993), Commander’s Commander's Cross with Star of the Order of Polonia Restituta(1993), Austrian Honorary Distinction for ‘Scientific and Artistic Achievements’, Pro Baltica Award (1995), Commandeur dans l'Ordre des Arts et des Lettres (1996), Duisburg Music Award (1999), AFIM Indie Award (1999), MIDEM Classical Award for Best Living Composer of the Year (2000), Ordine al Merito della Repubblica Italiana (2000), Premio Principe de Asturias de las Artes (2001), Award of the Great Foundation of Culture (2002), Romano Guardini Prize (2002), Preis der Europäischen Kirschenmusik (2003), Medal Fundacji Judaica (2003), Praemium Imperiale (2004), Order of the White Eagle (2005), Commander of the Three Star Order of the Latvian Republic (2006), Ministry of Culture Yearly Award, Józef Chełmoński Award, and Gold Medal of the Minister of Culture of the Republic of Armenia, the 2008 Orły Film Award for Andrzej Wajda’s Katyń, Grand-Croix de l’Ordre Pro Merito Melitensi (2011), the Ku Spotkaniu Award of the Marshal of the Senate of the Republic of Poland and the Chairman of the Federation Council of the Russian Federation (2011), the Badge of Honour for Contributions to Podlaskie Voivodeship (2013), and the Gold Medal of Honour for Contributions to Małopolskie Voivodeship (2013).
He has been granted honorary doctorates from the universities of Rochester, Bordeaux, Leuven, Washington, Belgrade, Madrid, Poznań, Warsaw, Buenos Aires, Glasgow, Kraków, Pittsburgh, Luzern, New Haven, Saint Petersburg, Leipzig, Seoul, Münster, Yerevan, Gdańsk, Kharkiv, and Maynooth.
He was an honorary member of the Royal Academy of Music in London, the Accademia Nazionale di Santa Cecilia in Rome, the Kungliga Musikaliska Akademien in Stockholm, the Akademie der Künste in Berlin, the Academia Nacional de Bellas Artes in Buenos Aires, the Académie Nationale des Sciences, Belles-lettres et Arts in Bordeaux, the Royal Academy of Music in Dublin, the American Academy of Arts and Letters, the Academia Scientiarium et Artium Europaea in Salzburg, the Institut for Advanced Study University, Bloomington, The Kościuszko Foundation in New York, the Gesellschaft der Musikfreunde in Vienna, the Academy for Performing Arts in Hong Kong, `Academia Argentina de Musica, Jāzeps Vītols Latvian Academy of Music in Riga, N. A. Rimsky-Korsakov Saint Petersburg State Conservatory, Moscow State Tchaikovsky Conservatory, and Komitas State Conservatory of Yerevan.
In 1997, he published a book entitled Labirynt czasu: Pięć wykładów na koniec wieku / The Labyrinth of Time: Five Lectures for the End of the Century (Warsaw: Presspublica, 1997). In 2013, the first edition of Krzysztof Penderecki Festival was held to mark the occasion of his 85th birthday. Five years later, in autumn 2018, the second Penderecki Festival took place.
At the 2013 Grammy Awards, Antoni Wit received the award for Best Classical Compendium category for the recording of the Polish National Philharmonic Symphony Orchestra's performance of Penderecki's Fonogrammi, Horn Concerto, Partita and The Awakening of Jacob and Anaklasis. Penderecki himself received five Grammy Awards in total (the 1968 Trustees Special Merit Award, 1988, two in 1999, 2017).