Matias' first coaching experience occurred with his Guarani, being in charge of the under-17 squad. In 2011, he joined Desportivo Brasil to become their under-17 coach, and won the 2012 U17 Campeonato Paulista with the side.[2]
Matias moved to Grêmio in 2014, again as an under-17 coach. On 20 February 2016, he signed for cross-town rivals Internacional under the same role,[3] and was appointed in charge of the latter's under-20s the following year.[4]
Matias left Inter on 23 February 2018,[5] and took over Figuerense's under-20s roughly one month later.[6] On 25 March 2019, he moved back to Internacional, again as coach of the under-20s.[7] With the latter, he won the 2020 Copa São Paulo de Futebol Júnior.[8]
On 26 February 2021, after the departure of Abel Braga, Matias was named interim head coach of the first team for the first rounds of the 2021 Campeonato Gaúcho.[9] His first match in charge occurred on 1 March, a 1–0 win over Juventude.
Matias subsequently returned to his previous role with the under-20s after Miguel Ángel Ramírez took over the main squad. On 21 July 2021, he was named head coach of Flamengo's under-20 side.[10]
Matias left Fla on 6 May 2022, and joined Red Bull Bragantino to work with the reserve and under-23 team.[11] On 8 January 2024, he moved to Botafogo to become the permanent assistant coach of their main squad.[12]
On 22 February 2024, Matias was named interim head coach of Botafogo, after Tiago Nunes was dismissed.[13] After just one defeat in ten matches, he returned to his previous role after the appointment of Artur Jorge.[14]
On 12 June 2024, Matias was named head coach of Série B side Coritiba.[15] On 23 July, after a 4–0 loss to Santos, he was sacked.[16]