Center Corey Linsley, with a knee issue, and tight end Donald Parham Jr., also with a hamstring injury, are questionable. Cornerback J.C. Jackson, who has been dealing with an ankle issue, and quarterback Justin Herbert, who has fractured rib cartilage, will play.
Allen suffered the hamstring injury in Week 1 and has not played since.
Earlier in the week, coach Brandon Staley expressed growing confidence that Allen might be able to return against the Texans.
However, on Friday, Staley said that Allen "kind of felt something" during individual drills at practice.
"We're going to hold him out of this game, just going to make sure that he keeps making progress," Staley said of the 10th-year pro. "Just don't want to push it where you have a significant setback of a major injury, so he couldn't make it this week and next week we'll give it another shot."
Staley added that Allen did not suffer a major setback. "Just didn't make enough progress to make it to the game," he said.
Allen has led the Chargers in receptions since 2017.
The Bolts are also without reserve wide receiver Jalen Guyton, who tore his left ACL on Sunday.