The Ivorian, signed for a club-record fee in the summer, was on the bench during Sunday's 2-2 draw with Norwich City at Carrow Road.
Speaking after the game, Ljungberg said: "Pepe is a very good player.
"Like I said, I try to look at what players have done in training and that's how I judge them."
On the game itself, Ljungberg added that he will start to work on the Gunners ailing defence.
"I think when we dominated the game, we had the possession and it wasn't a big problem.
"We have problem in transitions, and that's what I will try to fix.
"We want to be a club that has possession and hopefully when we have the ball and the opponents don't they can't shoot as much."