Andre Santos will also miss the game with an abdominal strain, manager Arsene Wenger told reporters on Tuesday.
Left-back Kieran Gibbs and Ivory Coast forward Gervinho return from injury and are in the squad, who are buoyed by their 5-2 win over Spurs.
Montpellier have injury concerns of their own with Benjamin Srambouli (virus), injured forward John Utaka, full-back Garry Bocaly and suspended striker Souleymane Camara all missing.
"He [Walcott] injured his shoulder in the game and we have to scan that and see if there is no damage. It should be short-term," Wenger said.
"We will miss Andre Santos as well as he has a muscle strain in his abdomen."
Wenger also praised his German defender Per Mertesacker, who scored his first goal for the club against Spurs on Saturday and has been playing well after enduring some criticism last season.
"To his defence I must say last year he arrived on August 31, and had no pre-season, had an ankle injury and had to adapt to a completely new world," the Frenchman told reporters.
"Centre-back is difficult for people who come from abroad, it was a bit of a shock for him, but this season he has come back very fit, well prepared, and of course knew what the expectations were for him and did extremely well.
"This season especially, as you [the media] have noticed, he has been outstanding. The criticism was always completely unjust. It was overboard, we always say you have to deal with that."
Despite a home defeat and an away draw with Schalke 04, Arsenal are second in Group B behind Schalke with two games remaining and will qualify for the last 16 if they beat Montpellier and Olympiakos lose to the Germans.
Schalke, who top the group with eight points, one clear of Arsenal, will advance if they defeat Olympiakos (six points) on Wednesday but if the Greek champions avoid defeat in Germany, they will still have a chance of going through when they host Arsenal in their last group match on December 4.
