After retiring, Bustos worked as an assistant manager before becoming a manager in 2009, with Manta. He continued to manage in Ecuador, winning two Ecuadorian Serie A titles with Delfín and Barcelona SC before being named in charge of Brazilian club Santos in 2022.
After being an assistant manager at Sarmiento, El Porvenir and Acassuso, Bustos was named manager of former side Manta on 15 July 2009.[2] He opted to leave the club on a mutual agreement on 8 December 2010,[3] and was named manager of another club he represented as a player, Deportivo Quito, thirteen days later.[4]
Bustos was sacked by Quito on 1 May 2011,[5] and was presented as manager of fellow Serie A team Imbabura on 30 June.[6] He resigned on 25 August,[7] and took over Técnico Universitario for the ensuing season on 16 December.[8]
Dismissed by Técnico Universitario on 14 April 2012,[9] Bustos was later named manager of Macará on 9 July.[10] He resigned from the latter on 28 April 2013,[11] and subsequently returned to Manta on 1 July.[12] After leaving Manta at the end of his contract in December 2013, Bustos was later named manager of Serie B side LDU Portoviejo.[13] He left the club the following 21 August.[14]
Delfín
He was named in charge of fellow second division side Delfín on 3 January 2015.[15] He led Delfín back to the top tier after 15 years, but was dismissed by the club on 30 April 2016.[16] Bustos returned to the club in December 2016, now as a sporting director,[17] but was named manager again in April 2018, after the departure of Guillermo Sanguinetti.[18] He stayed in charge of Delfín for the following season, in which the team finished in 4th place of the first stage of the 2019 Serie A, advancing to the playoffs. After defeating Independiente del Valle, Macará and L.D.U. Quito in the final, Bustos led Delfín to their first-ever Serie A title; however, he left the club on 15 December of that year.[19]
Barcelona SC
Immediately after leaving Delfín, Bustos took over Barcelona SC.[19] In his first season, he won a second consecutive Serie A title, and led the club to the semifinals of the 2021 Copa Libertadores.
On 25 February 2022, Barcelona announced Bustos' departure through a press conference, with his last match in charge of the club occurring the following day.[20]
Santos
On 25 February 2022, Santos announced the signing of Bustos as manager, with his contract to be signed in the following days.[21] On 7 July, after just one win in 13 matches, he was sacked.[22]
Return to Barcelona SC
On 5 September 2022, Bustos returned to his former club Barcelona in the place of departing Jorge Célico.[23] He resigned on 4 June of the following year, after a 3–1 loss to rivals Emelec.[24]
América Mineiro
On 9 August 2023, Bustos returned to Brazil and its top tier, after being named head coach of América Mineiro.[25] On 9 November, after the club's relegation, he was dismissed.[26]
Bustos' older brother Carlos is also a manager and former footballer.[28] A defender, he began his career at Talleres and had the most of his managerial career in Peru and Mexico.
^"Abandona el Atunero" [He leaves the Tunamen] (in Spanish). Futbol Ecuador. 8 December 2010. Archived from the original on 12 December 2010. Retrieved 20 February 2022.