The reigning European champions must overcome the challenge of United if they are to defend their crown after the duo were paired together in Friday's quarter-final draw.
In contrast to their last-eight place in the competition, United have endured an indifferent league campaign and sit seventh in the standings.
However, Kroos says that it would be a mistake to underestimate David Moyes's men based on their domestic tribulations.
The Germany international wrote on his Facebook page: "A very interesting draw for us! We shouldn't measure Man U by their current position in the English table."
The 24-year-old, who has been heavily linked with a summer move to Old Trafford, travels to the North-West with Bayern for the first leg on April 1 before welcoming the English giants to the Allianz Arena eight days later.