Xaghra United and Sannat Lions made it to the second round after beating Third Division sides Kalkara and Sirens.
SK Victoria Wanderers defeated fellow Gozitan side St. Lawrence Spurs while Fgura United beat Marsa 2-1.
At the Gozo Stadium, Xaghra United beat Kalkara 2-1.
Thiago Dos Santos put Xaghra ahead on 43 minutes but Justin Farrugia levelled matters on 68 minutes but two minutes in added time, Michael Bezzina notched the winner for Xaghra.
In the second round, Xaghra will be facing Second Division side Siggiewi.
In another match at the Gozo Stadium, SK Victoria Wanderers defeated St. Lawrence Spurs 2-0 thanks to goals by Kenneth Mercieca and Matthew Zammit.
The Wanderers face Gzira United in the second round.
At the Luxol Stadium, Gozitan champions Sannat Lions beat Sirens 4-1. This was the first game from the FA Trophy to be played at one of the regional stadiums which is being used as from this season for senior competitions.
New Sannat signing, Diego Maradona Petriaggi, who joined the club from Mosta, scored two of the goals and Eric Chidi Nwankwo added another two. Jonathan Grech scored a consolation goal for Sirens.
On the other hand, Fgura United defeated Marsa 2-1 thanks to a brace by Michael Zammit with Yusif Abdullah scoring the only goal for Marsa.
Fgura will be meeting Msida St. Joseph in the next stage.