On 29 January 2015, Franck Kessie signed a three-year contract with Serie A club Atalanta. He was assigned to the club’s Primavera squad upon his arrival, and contributed with seven appearances for the side. His first match in Europe occurred on 1 March, as he started in a 2–0 away win against A.C. Milan Primavera.
On 18 April 2015, Franck Kessie was called up to the first team for a match against Roma, but remained an unused substitute in the 1–1 draw the following day.
On 26 August 2015, Franck Kessie joined Cesena in the Serie B on a one-year loan deal. He made his professional debut on 26 September, coming on as a substitute for Antonino Ragusa in a 0–0 away draw against Perugia.
Kessié scored his first professional goal on 31 October 2015, netting the last in a 2–0 home win against Virtus Lanciano. He became an undisputed starter afterwards, appearing in 37 matches and scoring four goals as his side missed out promotion in the play-offs.
Return to Atalanta
After returning from loan, Franck Kessie was promoted to the first team by manager Gian Piero Gasperini. After appearing with the main squad during the pre-season, he made his debut for La Dea on 13 August 2016, starting and scoring the last in a 3–0 Coppa Italia home win against Cremonese. Six days later, he renewed his contract until 2021.
Kessié made his debut in the main category of Italian football on 21 August 2016, as he started and scored a brace in a 4–3 home loss against Lazio. He scored another goal seven days later, in a 2–1 away defeat to Sampdoria.
Franck Kessie subsequently became a mainstay in Gasperini’s starting eleven, scoring the winners against Torino (2–1 home win) and Roma (2–1 home win), both through penalties. He also scored the equalizer against Empoli on 20 December 2016, with Marco D’Alessandro scoring a last-minute winner.