Koscielny ruptured his Achilles in Arsenal's Europa League defeat against Atletico Madrid last season.
The 33-year-old missed France's World Cup-winning campaign due to the injury.
He finally returned for Arsenal's reserves in a Checkatrade Trophy clash with Portsmouth last week and Emery confirmed on Wednesday that Koscielny will start against Qarabag.
The Gunners have a defensive crisis ahead of Sunday's trip to Southampton with Rob Holding injured, Shkodran Mustafi struggling with a hamstring problem and Sokratis Papastathopoulos suspended.
That could mean Koscielny will be asked to play twice in four days if he proves his fitness.
"Because we are going to play a lot of matches, in the next 10 days we play four matches - each of them very important...it is in our planning to start with Laurent Koscielny," Emery told reporters.
"We are going to decide after tomorrow's match, as it's the first match with us that Laurent Koscielny will play. We are going to look also if he can play 90 minutes or less minutes in this game.
"We are going to decide but the first is to think about the match tomorrow because we need to receive information on how he can feel."
Mesut Ozil could also feature against Qarabag having lost his place in Emery's Premier League side.
Germany midfielder Ozil has missed the last five games in all competitions with a combination of a back injury and Emery preferring other options in his starting line-up.
Emery was forced to deny reports of a training ground row with Ozil earlier this season after claims he had told the former Real Madrid star to work harder.
"Tomorrow he is in the group, there are 18 players in the squad for this match and I am going to decide if he plays tomorrow from the beginning or during the match in the 90 minutes," Emery said of Ozil.