Floriana will be facing a trip to Croatia to face giants Dinamo Zagreb should they seal a Europa League play-off berth following the draws, held in Nyon, on Friday.
The Maltese champions defeated Linfield in a historic night in Belfast to advance to the third qualifying round of the competition, on Thursday.
The Greens joined Birkirkara and Valletta in becoming Malta’s third ever team to make it this far in the Europa League.
Floriana will host Estonia side Flora Tallinn at the Centenary Stadium, next Thursday.
Dinamo Zagreb started this year’s European campaign in the Champions League but after defeating Cluj in the second round, they were dumped out by Ferencvaros in the following qualifier.