Emery admitted his belief that his side will be without first choice full back Hector Bellerin for 'a few weeks' after the Spaniard sustained a suspected calf injury this weekend.
23 year old Bellerin managed to hobble on until the interval against the 'Saints', but he did not emerge for the second half of the match.
This latest set back comes after centre half Rob Holding was ruled out for the remainder of the season, thanks to knee ligament damage suffered in the draw against Manchester United last week.
Arsenal were handed a boost with the return of Frenchman Laurent Koscielny this week, after considerable time on the treatment table himself. But they were still forced to deploy full back Stephan Lichtsteiner at centre half on Sunday.
After the defeat to Southampton, boss Emery told the media: "He [Bellerin] has one small injury but I think he will be some weeks off. Sokratis is coming back, as are Mustafi and Kolasinac."
The loss to the south coast side brought an end to an incredible 22 match unbeaten run for the North London side, and was only Southampton's second home league win in over a year.
Emery's men will have to recover fast, as their next match is a mouthwatering North London deby clash with Tottenham, in the Carabao Cup quarter-finals on Wednesday,