The England international sustained the problem at the weekend during Arsenal's 5-2 derby win over Tottenham Hotspur.
But Walcott was able to play on and scored the Gunners' fifth goal in injury time at the end of the match.
Arsenal boss Arsene Wenger revealed Walcott had not trained on Tuesday and would have a scan to determine the extent of the injury, although he thought it would be short-term.
But the Gunners have been boosted by the news Gervinho and Kieran Gibbs are fit to return to the squad, although Andre Santos has been ruled out.
Wenger said: "The injury he got during the game with his shoulder, we have to scan that today and see if there is no damage. He will be out for tomorrow. It should be short-term.
"We will miss Santos as well, who has a muscle strain in his abdomen. The two players coming in the squad are Gervinho and Gibbs."
Arsenal will hope to overcome the absence of Walcott and Santos and qualify for the knockout stages if they defeat Montpellier and Schalke beat Olympiakos.
And so boss Wenger is demanding full focus from his squad, as he said: "First [we want] to qualify. It's important that we show another good performance.
"There's no risk that this team is complacent. The team will be full of desire to do well and win."