Welbeck was stretchered off after just 25 minutes of their goalless draw against Sporting Lisbon with a serious-looking injury while challenging for a header and he landed badly on his right ankle.
The 27-year-old was administered oxygen on the pitch and his leg was put in a protective boot.
After the game, the former Manchester United striker was rushed to the hospital and further tests will be undertaken to assess the extent of the injury.
And Emery confirmed the problem after the match.
“It’s his ankle. He’s broken something in his ankle,” Emery said.
When discussing the players’ reaction to the injury, he said: “When a player has an injury like that the players look and in your mind you feel for the player.
“Then the players concentrated on the match and we forgot.
“When we finished the match the first thing was to ask about him.”
Arsenal’s draw with Sporting means they have qualified for the knockout stages of the Europa League.
And Petr Cech revealed his delight after the match.
He said: “It was down to them working well, they were very organised and have very good players so you have to control our emotion, and we lacked a little bit of the killer pass.
“We know we need to switch back to the Premier League and then we look to finish the job in Ukraine.
“It is tough when you are the favourites in the group and everyone plays with extra motivation against you.”
The Gunners turn their attentions back to the Premier League on Sunday (4.30pm) when they host Wolves.