In 2017, as a freshman at USM, Wallner hit .336 with 19 home runs and 63 RBIs in 66 games. He also appeared in nine games out of the bullpen, compiling a 1.84 ERA.[7] He was named conference Freshman of the Year by Conference USA (C-USA), Baseball America, and D1Baseball.com.[8][9] He also garnered Freshman Hitter of the Year honors from the National Collegiate Baseball Writers Association.[10] In addition, he was named to the C-USA All-Freshman Team as well as the C-USA Second Team, and was also named a Freshman All-American by multiple outlets including the Collegiate Baseball Newspaper and the National Collegiate Baseball Writers Association.[11][12]
As a sophomore in 2018, Wallner batted .351 with 16 home runs and 67 RBIs in 62 games while recording a 7.98 ERA in 14+2⁄3 innings.[13][14] He was named to the C-USA First Team and once again was named an All-American by various publications.[15][16] Following the season, he played for USA Baseball as a member of the Collegiate National Team.[17] He also played in the Cape Cod Baseball League for the Falmouth Commodores.[18][19]
Prior to the 2019 season, Wallner was named a preseason All-American by Baseball America, Collegiate Baseball Newspaper, D1Baseball.com and Perfect Game.[20][21] During the year, he hit his 54th career home run, becoming USM's all-time record holder.[22] Wallner batted .323 with 23 home runs and sixty RBIs for the season, earning a spot on the C-USA First Team.[23][24] He finished his collegiate career with a school record 58 home runs.[25]
To begin the 2021 season, Wallner returned to Cedar Rapids, now members of the High-A Central.[33] In late May, he was placed on the injured list with a right wrist sprain.[34] It was later revealed that he broke a hamate bone and required surgery.[35] He was activated on July 20.[36] Over 68 games with Cedar Rapids, Wallner slashed .265/.350/.504 with 15 home runs and 47 RBIs.[37] He was selected to play in the Arizona Fall League for the Scottsdale Scorpions after the season.[38] Wallner was assigned to the Wichita Wind Surge of the Double-ATexas League to begin the 2022 season.[39] He was selected to represent the Twins at the 2022 All-Star Futures Game.[40] In mid-July, he was promoted to the St. Paul Saints of the Triple-AInternational League.[41] Over 128 games played between Wichita and St. Paul, he slashed .277/.412/.541 in 458 at bats with 27 home runs, 95 RBIs, and 32 doubles, and was third in the minor leagues with 97 walks.[42][43]
On September 17, the Twins selected Wallner's contract and promoted him to the major leagues.[44] He made his MLB debut that night, hitting a solo home run off of Shane Bieber of the Cleveland Guardians for his first MLB hit.[45]
Wallner was optioned to Triple-A St. Paul to begin the 2023 season.[46] He was called up to the majors for the first time in early April and went hitless in six games between April 8–15. He was recalled from Triple-A again on May 23 after Trevor Larnach contracted pneumonia.[47]