In 2013, Matonense won, for the second time, the Campeonato Paulista Segunda Divisão. With the best campaign since the first stages of the championship, Matonense reached the final against Água Santa de Diadema. However, Matão's team was beaten in ABC Paulista by 5x2, forcing them to win an expressive victory by more than 3 goals difference and in a historic game, Matonense made 4x0 and guaranteed the second championship of the second division, after 18 years.
In 2014, Matonense guaranteed access to the A2 division of Paulistão together with the champion of this edition in the same group, Grêmio Novorizontino.
In 2015 Matonense was relegated in the Campeonato Paulista A2 division, ending the championship with 17 points, being in 18th place.
In 2016 the club returned to the A3 division, finishing the first phase in 5th place, with his technical team formed by trainer Pinho and as a technical assistant Anderson Florentino.