After retiring, Gandolfi started working as an assistant of his last club Talleres. On 6 September 2022, he was named interim manager after the departure of
Pedro Caixinha. Gandolfi was confirmed as Talleres manager for the 2023 season on 1 November 2023. He left the club on 27 November 2023, after opting to not renew his contract. On 20 December 2023, Gandolfi replaced compatriot
Martín Anselmi at the helm of
Ecuadorian Serie A side
Independiente del Valle. Despite reaching the finals of the
2024 Serie A and
2024 Copa Ecuador, Gandolfi was sacked on 17 December 2024 after losing both of them. On 20 January 2025, Gandolfi was announced as manager of
Categoría Primera A club
Atlético Nacional. He was dismissed on 16 September 2025, following a defeat to
Atlético Bucaramanga in which he fielded four foreign players simultaneously, breaching league regulations which only allow teams to field up to three non-Colombian players at the same time. ==Managerial statistics==