During his time in La Liga the Chilean was in the opposing dugout to former Barcelona coach Guardiola on eight occasions and only avoided defeat once when his Villarreal side drew 3-3 in the Nou Camp in the 2008-09 season.
His brief stay at Real Madrid included two El Classico defeats by Guardiola's Barca and the trend continued at Malaga where he soaked up another four losses against the Catalans.
The furniture has been re-arranged in European soccer, however, and Pellegrini will feel his expensively-assembled Man City side will start as equals to Bayern who have yet to really spark under Guardiola even if they are unbeaten.
Pellegrini was head-hunted by City at the end of last season partly because of his tactical nous in the Champions League in which he had Villarreal and Malaga punching above their weight.
He has never failed to survive the group stage in his previous Champions League campaigns and City's opening day 3-0 win away to Viktoria Plzen has raised hopes that they can finally make their mark on the competition having twice fallen short of the knockout rounds.
Despite that emphatic victory in the Czech Republic Pellegrini's opening weeks in charge of City have been far from smooth with two defeats in their opening six Premier League games, the latest a 3-2 loss at Aston Villa on Saturday.
Pellegrini was baffled by his side's loss at Villa, having dominated for long spells, but said it would have no adverse effect on morale ahead of a visit from the European champions.
"It's always better to play in the Champions League when you have won the Premier League game before but the team is playing with trust and confidence so I hope we can do a good match again next Wednesday," he said.
"In general, I was very happy with the way we played."
City could be boosted by the return of midfielder David Silva who has been out since the end of August.
Guardiola's start at treble-winning Bayern has been efficient rather than spectacular with Saturday's 1-0 win at home to VfL Wolfsburg indicative of their form so far.
"It is very difficult at this moment to improve with Bayern because they won the last three competitions but he will find a way because he is a very good manager," Pellegrini, who does not have that dilemma at City, said.
Bayern began the defence of their European crown with a 3-0 home win against CSKA Moscow and there are already signs that the Bundesliga giants are playing a more intricate, possession-based game than under the more direct Jupp Heynkes.
Against CSKA Bayern completed 753 passes, more than any other team in the opening group games, and Bayern are unlikely to change that blueprint throughout the campaign, even if Guardiola admits his side have room for improvement.
"We need to do some things better even though we won against Wolfsburg," Guardiola, who won 14 trophies in four seasons in charge of Barcelona, told reporters. "I am certain we will put in a good performance against Manchester."
Bayern lost to City two years ago when they had already qualified for the last 16 and defender Jerome Boateng, formerly of City, believes under Pellegrini the Premier League side can be even more of a threat in Europe.
"I think so they are stronger, new coach, changes in tactics. They play even better together now. Not like two years ago. They are more of a team," he said. (Reporting by Martyn Herman, editing by Pritha Sarkar)