The Bavarians, chasing three titles this season, are without Arjen Robben, Franck Ribery, Bastian Schweinsteiger and David Alaba among others for the quarter-final first leg in Portugal.
"For the (recent) games against Borussia Dortmund and Bayer Leverkusen we had two matches where we played with a decimated squad and with few options," Mueller told reporters.
Bayern beat Dortmund in the Bundesliga before edging past Leverkusen in the German Cup last eight on penalties and looked unaffected by the absences. They also beat Eintracht Frankfurt 3-0 on Saturday.
"In those games we came closer together as a group, as a unit, and that will obviously help us against Porto," said Mueller.
"Now it is not about the injuries but about building a strong unit on the pitch with the players who are there. We are confident and hopefully we can score a few goals."
Five-times champions Bayern will rely heavily on the scoring prowess of Mueller and Robert Lewandowski in the absence of Robben and Ribery as they look to become the first team to beat Porto in the Champions League this season.
Twice winners Porto won four matches and drew twice in the group stage before crushing Basel 5-1 on aggregate in the round of 16.
"I am surprised with their level and we will need two good games to reach the semi-finals," said Bayern coach Pep Guardiola.
"They play an open game ... they have physical midfielders but with great quality. That is also their biggest asset. Their individual quality."
Guardiola added there was no point talking about the Bayern injuries, saying he would simply try his best with the players at his disposal.
"The last two weeks we talked about this a lot but we have this situation and we are here with these 14 players and we will try our best. That's what it is and I won't complain," he explained.
(Reporting by Karolos Grohmann, editing by Tony Jimenez)
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