The defending champions are top of Group D with six points from two games while their Czech opponents are bottom and yet to register a point while already having conceded six goals.
It would appear to be a straightforward victory for the Bundesliga champions but Guardiola is having none of it.
Quoted on the club's official Twitter feed, Guardiola said: "We have great respect for the opponents' counter-attacking.
"Against Manchester City they played very well in the first half."
Bayern opened their campaign with a 3-0 home win over CSKA Moscow before registering a highly-impressive 3-1 victory at Manchester City in their previous outing.
With CSKA and City facing each other, Bayern are well placed to take advantage of a stalemate between the pair and further extend their lead.
Captain Philipp Lahm said: "We are in a very, very good position with six points from the first two games, now we want to add more."
Guardiola revealed that Franck Ribery had trained "very well" on Tuesday and a decision would be made on Javi Martinez after the pair had been doubtful with ankle and groin injuries respectively.
Plzen have found it tough going. Three goals in 10 second-half minutes saw them go down to a 3-0 home defeat by Manchester City in their first match although they were only edged out 3-2 against CSKA Moscow.
Goalkeeper Matus Kozacik is under no illusions as to the magnitude of the task facing his side and was effusive in his praise of the Germans, comparing them favourably with Guardiola's former team Barcelona.
He told his club's official website: "Bayern are certainly the best team in the world, they managed to win last season in domestic competition and the Champions League.
"It seems to me that they (Bayern and Guardiola) are a great combination and they are even stronger than Barcelona.
"When I saw their match with Manchester City, I was really impressed with Bayern's excellent performance.
"Naturally, we know what a difficult match awaits us.
"We appreciate the opportunity to play against the best teams in the world and we believe that we will do everything (to get a) good result, demonstrating commitment to Plzen."