The Brazil international returned from a groin injury off the bench in the North London derby victory over Tottenham Hotspur at the weekend, where Kai Havertz led the line with support from Leandro Trossard.
However, Trossard has now been demoted from the starting XI to make room for Jesus, meaning that Havertz will presumably play in the number 10 role vacated by the injured Martin Odegaard.
Jesus's return is one of two changes that Mikel Arteta has made to Arsenal's starting lineup in Bergamo, as Declan Rice unsurprisingly comes straight back into midfield following his Premier League ban.
Jorginho is the one to make way for the Englishman, and the Arsenal backline is unchanged, as Jurrien Timber continues at left-back despite the return of Riccardo Calafiori from a calf issue.
The Italian has only made the bench for Arteta's side as he awaits his first competitive start for the Gunners, but Bukayo Saka starts as expected, having shaken off his knock from the weekend.
Ex-Arsenal man helms Atalanta defence
However, Oleksandr Zinchenko, Kieran Tierney, Mikel Merino and Takehiro Tomiyasu are still absent for Arsenal, who have five current academy products on the bench alongside Chelsea loanee Raheem Sterling.
Meanwhile, Atalanta boss Gian Piero Gasperini has made just the one change to his side from their 3-2 Serie A win over Fiorentina last time out, bringing in Davide Zappacosta for Raoul Bellanova at right wing-back.
A familiar face starts as part of the Dea back three, as erstwhile Arsenal defender Sead Kolasinac reunites with the team he made 118 appearances for between 2017 and 2022.
Europa League hat-trick hero Ademola Lookman forms part of a menacing front three with Charles De Ketelaere and Mateo Retegui, all of whom scored in the weekend's win over Fiorentina.
Highly-rated midfielder Ederson joins the long-serving Marten de Roon in the hosts' engine room, while veteran winger Juan Cuadrado - still going strong at 36 - is among the substitutes.
Atalanta BC: Carnesecchi; Djimsiti, Hien, Kolasinac; Zappacosta, De Roon, Ederson, Ruggeri; De Ketelaere, Retegui, Lookman
Subs: Patricio, Rossi, Kossounou, Cuadrado, Pasalic, Zaniolo, Bellanova, Samardzic, Palestra, Brescianini, Vlahovic, Del Lungo
Arsenal: Raya; White, Saliba, Gabriel, Timber; Havertz, Partey, Rice; Saka, Jesus, Martinelli
Subs: Neto, Porter, Kiwior, Trossard, Sterling, Jorginho, Calafiori, Butler-Oyedeji, Gower, Nwaneri, Lewis-Skelly, Oulad M'Hand