The Italian champions face Juventus in Serie A at the weekend and reports had suggested that Allegri will rest a number of players ahead of that match.
However, the coach has revealed that he will select his "strongest team" at the San Siro.
"I'll put out my strongest team, then we'll start thinking about Juventus on Thursday," Allegri told Gazzetta dello Sport.
"[Plzen are a] well-drilled unit, technically sound and very quick on the wings.
"As it's never easy to win matches, we'll have to face them with the right amount of determination."
Milan opened their European campaign with a 2-2 draw against Barcelona.