Captain Laurent Koscielny made his first appearance of the season in Thursday's 1-0 win over Qarabag in the Europa League.
The 33-year-old suffered a ruptured Achilles in May that ruled him out of France's triumphant World Cup campaign.
Koscielny completed 72 minutes alongside Sokratis Papastathopoulos but the luxury of deploying two specialists at the heart of his defence is not one Emery will enjoy at St Mary's.
Sokratis is suspended after collecting a fifth booking in 10 Premier League appearances against Huddersfield Town last weekend, while Shkodran Mustafi is recovering from a hamstring strain and Rob Holding's season is over following cruciate knee ligament surgery.
It makes the risk of asking Koscielny to go straight back into action all the more acute, with full-backs Stephan Lichtsteiner and Nacho Monreal and midfielders Granit Xhaka and Mohamed Elneny among the possible options for the heart of defence.
“My game is over, my season is over, my World Cup is over.”— Arsenal FC (@Arsenal) December 14, 2018
Seven months away from the pitch, seven months of intensive work, seven months to fight for his career.
This is the story of @6_LKOSCIELNY: STRONGER
"Now we will think for Sunday. We haven't got Mustafi, Holding or Sokratis but I believe in my players, in our players, and I think we can use other players [as] centre-backs.
"I have one idea in my mind but we need to [work in training] and to know how they will recover physically, for the possibility of playing on Sunday.
"I think every player is now okay to help us in the position we need."
Mesut Ozil returned to action in midweek following his recent back troubles, while Emery expects fellow attacking midfielder Aaron Ramsey to be recovered from an ankle injury.
"After his injury he came back with good work, he gave the performance and I think he's okay for Sunday," the head coach said of Ozil
"We think yes [Ramsey will be available]. The doctor said to me he thinks on Saturday he can train and be okay for Sunday."