The forward was part of the Bayern Munich side that cruised to a 3-0 aggregate victory over Messi and Paris Saint-Germain in the Champions League midweek.
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That victory extended Muller's impressive record against the World Cup winner, with the 33-year-old Bayern star beating Messi in eight of their nine meetings, including the 2014 World Cup final when Germany came out on top.
In stark contrast, Ronaldo came out victorious five times out of eight matches with Bayern while playing for Real Madrid, scoring a staggering nine goals in the process.
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So while Muller was full of praise for Messi, he simply pointed out things have worked out better for him when facing him at club level.
With a smile on his face, he said: "Against Messi, things always go well at all levels in terms of results.
"At club level, Cristiano Ronaldo was our problem when he was at Real Madrid."
However putting jokes aside, Muller spoke of his admiration for Messi, adding: "I have the greatest respect for Messi's World Cup performance.
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"His individual performance was amazing. He carried the whole squad. It's not so easy to play at a team like PSG. It's difficult to get a really good team balance."
Messi's future in the French capital is uncertain.
He has been linked with a move away from Europe to MLS side Inter Miami.
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Ronaldo, meanwhile, has already left the Continent and is plying his trade at Al Nassr in Saudi Arabia, meaning Muller could add a third Champions League winners medal to his collection.
He won with Bayern in 2013 and 2020.