Przemek narrowed his decision down to California and Gonzaga. He committed to Gonzaga on May 29, 2012. For his freshman season he was behind star Canadian center Kelly Olynyk, a future lottery pick in the 2013 NBA draft. In the 2013-14 season Karnowski averaged 10.4 points, 7.0 rebounds and 1.7 blocks per game as the Bulldogs' starting center. As a junior, he averaged 11 points, 5.8 rebounds and 1 block per game. Due to back problems, Karnowski had surgery after playing only five games in his senior season. He was averaging 8.8 points and 5.4 rebounds in those five games. The surgery followed a prolonged episode of back pain so severe that by the time of the operation, it took him over an hour to get out of bed and perform normal morning activities; he was also unable to walk without crutches. He developed an infection after undergoing the surgery and lost roughly. Karnowski's recovery proceeded ahead of schedule; while he was told he would be unable to perform any strenuous activities for 10 months post-operation, he was running after 7 months. For the rest of his Gonzaga career, the team's training staff placed him on a customized conditioning program to protect his back, and he did not participate in any basketball-related activity outside of games and scheduled practices. On May 24, 2016, Gonzaga announced that Karnowski had received a medical redshirt and would return to the school for one final college season in 2016–17. In his final season with Gonzaga he led Gonzaga to the best start in the history of the organization whilst posting the best offensive and defensive numbers of his career: 12.4 points, 5.8 rebounds, 2.0 assists and 0.9 block in just 22.5 minutes per game coming to the tournament. On February 2, 2017 Karnowski became the career leader in wins for Gonzaga, passing Kevin Pangos and Kyle Dranginis. Following the game with BYU, Karnowski became the active leader in Division I basketball games played with 143, passing Nigel Hayes, Nate Britt and Isaiah Hicks. Karnowski would be surpassed later that season by Hayes and Duke'sAmile Jefferson, and passed both in a win in Gonzaga's Final Four matchup with South Carolina. After the 2017 West Coast Conference Men's Basketball Tournament, Karnowski became the NCAA's career leader in wins with 132, passing Shane Battier. During his senior season he was nominated to the Kareem Abdul-Jabbar Award and Senior CLASS Award. Karnowski graduated with Bachelor of Education in Sport Management and MBA with one of the highest GPAs in WCC, for which he was named to the 2016-17 WCC Men's Basketball All-Academic Team. With 13 points performance and two crucial baskets he led his team to a 77-73 victory in the NCAA tournament semifinal, giving the Gonzaga Bulldogs their first ever appearance in the NCAA March Madness Final. During his tenure with Gonzaga Bulldogs he became a fan favorite not only because his skills, but also because of his outgoing and friendly attitude as well as his signature beard. Some fans even wear fake beards during games to impersonate Karnowski. His name is found difficult to spell for basketball fans from the USA, thus he was given fancy nicknames like "Shem", "Big Shem," or "Mount Karnowski". His performances are also widely recognized in his country, Poland. Tens of thousands of Polish fans watched his March Madness surge overnight, because of the time difference.
