Guardiola will miss the next two top-flight games after the routine operation, with Lillo taking his place on the touchline up until the upcoming international break.
The assistant manager returned to Man City earlier this month as he rejoined the club's backroom staff following a spell as boss at Qatari side Al Sadd.
Lillo has now been tasked with leading the treble winners through the next two fixtures, so talkSPORT.com takes a look into his career.
Who is Juanma Lillo?
Lillo has been involved in coaching for 42 years, beginning his career at the age of just 16 with a local team in Spain.
He then took his first managerial job four years later and that was only the start as he took charge of 12 different teams across world football over the next 20 years.
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In 2015, Lillo took a step back from being the boss and become assistant at Chile under Jorge Sampaoli before moving on to be his No.2 at Sevilla a year later.
He then had spells as manager of Atletico Nacional in Colombia, Vissel Kobe in Japan and Qingdao Huanghai in China.
The call from Guardiola would then follow and he joined Man City, replacing Mikel Arteta as his assistant boss in 2020.
Lillo was Pep's manager when he played for Mexican side Dorados de Sinaloa in 2006 and the City boss admitted he learnt a lot from the Spaniard.
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Guardiola told Sky Sports: "It was a good school.
"I was a player also focused on playing but his ideas on the bench about progression, how he prepared the games and the training sessions, were so important for me.
"I felt that in that moment of my career, I needed a guy who would help me to see something I was not able to see. Working with him in Mexico helped me to improve."
Lillo spent two years with Pep at City before leaving to become first-team coach for Qatari side Al Sadd.
During his time in the Middle East, the 57-year-old revealed his thoughts about the state of modern football and took aim at managers despite him being one himself…
Speaking to The Athletic, he said: "Football's finished and now whatever this is has emerged, I don't dare name it.
"The purpose of the game has been subverted - now they're looking more for consumers than fans, the industry needs TV money.
He continued: "The best players come together for international football and, thank God, they're not trapped by the omnipotence of the manager, because there's no time to coach.
"It really is wonderful because we, the managers, have too much influence. It's unbearable.
"We have our own ideas and we say that we espouse them to help people to understand the game. Bull****! It should be for the players to understand the game as they understand it."
These comments will confuse many considering Lillo himself has been a manager for decades, but his different mentality towards coaching is what Guardiola admires.
And that's why he asked Lillo to rejoin his backroom staff before the start of this season following the departure of Enzo Maresca.
"Juanma sees things no one else in the game sees," Pep said after reappointing his assistant last month.
"He understands football on an incredible level, so he is the perfect person for me to work alongside.
"I have always been inspired by him - his knowledge of football, his intelligence and his humanity mark him out as a very special person in my life - and we have a shared ideology.
"He is a friend, a colleague and an inspiration. I am so, so happy he is back here at Manchester City.
"His preparation for matches is absolutely amazing. I know he will raise standards because he works so hard every single day."
City's Director of Football Txiki Begiristain also believes that Lillo's vision is 'totally aligned with Pep's' which shows why he has been trusted to take over.
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Lillo will be on the touchline in the Premier League up until the international break with fans set to get a closer look at the assistant over the next few weeks.
And with him being held in such high regard by Guardiola, the champions are set to be left in good hands.