Matos assisted Filipe Coelho at
Leixões S.C. and Vilafranquense, and became manager of the third-tier latter side in December 2017 when his mentor moved abroad. He debuted on 10 December with a 2–0 away win against
GS Loures, and finished
the season as runners-up to
C.D. Mafra before elimination in the play-off semi-finals by
S.C. Farense (4–1 aggregate). On 6 March 2019, Matos was replaced in his job by Filipe Moreira. Three months later, he was appointed at nearby
F.C. Alverca in the same league. On 17 October, he led them to a 2–0 home victory over Sporting in the
third round of the
Taça de Portugal, only the second time that the opposition had been eliminated by a third-division club. He left by mutual consent on 27 December. Matos returned to the game on 5 July 2020 at
Casa Pia AC, who had been kept in division two on a court decision. He left his post still during pre-season, but remained with the team as an assistant manager. On 20 June 2023, Matos departed this role at the now top-flight
Lisbon club, to take the helm at newly relegated
C.D. Santa Clara. He won promotion in his
debut campaign as champions, with a record point tally of 73, no matches lost away from home and the best defence in the top ten European leagues at only 19 goals conceded. Matos and his team started
2024–25 on a high note. On 30 November, he oversaw a 1–0 win over Sporting, the
Azoreans' first at the
Estádio José Alvalade in history. They eventually finished a best-ever fifth, thus
qualifying for the
UEFA Conference League. On 31 January 2026, following a poor start to
the season that left the side just above the relegation zone, Matos was dismissed; in the club's official statement, he was referred to as "Santa Clara's greatest ever manager". ==Managerial statistics==