On 8 September 2020, he was appointed as the head coach of the club’s U-23 team, as well as the Academy’s director of methodology.

On 27 August 2021, Sartini took over as interim coach of the Whitecaps’ first team, after the sacking of Marc Dos Santos. On 29 August, Sartini took charge for the first time as Whitecaps’ head coach in their league match against Real Salt Lake, which ended in a 4–1 victory at BC Place. With the squad being at the bottom of the Western Conference’s league table at the time of his appointment, Sartini managed the side to seven wins, five draws and two losses until the end of the regular season, collecting a total amount of 26 points in 14 matches and helping the club qualify for the Playoffs, although the team eventually lost to Sporting Kansas City in the first round.

On 30 November 2021, Whitecaps announced that Sartini would officially become the club’s new head coach, having signed a contract until the 2023 season.

On 26 July 2022, the Italian manager won the first trophy of his career as Whitecaps won the Canadian Championship, following a 5-3 win (on aggregate) over Toronto FC after a penalty shoot-out in the final match.

On 8 June 2023, Sartini guided the Canadian team to their second Canadian Championship title in a row, thanks to a 2-1 win over CF Montréal in the final match.