The Ashanti regional champions defeated their opponents 1-0 in what was an exciting quarter-final clash at the Paa Joe Park.
Following a goalless first half, Amoawi Methodist upped their game in the second half and rightly opened the scoring towards the end of the game.
Amoawi reached the quarter-finals after winning Group D, while Babatokumaa Primary qualified to the knockout stage as runners-up in Group C.
Earlier in the day, St. Joseph Int. School and Bodaa R/C Primary qualified for the semis after defeating Akweiman D/A Primary and Krasec L/A Primary, respectively.
Meanwhile, Talent Bridge Academy are also in the semi-final after beating Kaladan E.P. Primary 3-0.
Amoawi Methodist will now face off with Bodaa R/C Primary in the semi-finals, while Talent Bridge Academy will also play against St. Joseph Int. School.
The final of the 2019 Milo U-13 Champions League will take place on Saturday.