When Pep Guardiola agreed to take over at Manchester City, one of the things that attracted him was the idea that his arrival at the Etihad Stadium would constitute Year Zero in the life of his new club.

At Bayern his methods were “counter-cultural” and met with resistance everywhere. The former Bayern players on TV complained that his team passed the ball too much, or the club doctor who had been there since the 1970s would tell him “this isn’t how we do things around here”. At City there would be no pre-existing culture to counter. He could build his ideal team and club effectively from scratch.

Except City have their history too, even if Guardiola wishes it were otherwise. City's fans feel as though their club has been unfairly treated by Uefa on issues such as Financial Fair Play, a system that they feel was designed specifically to make life difficult for Manchester City. And so the crowd at City seem to have decided they don't like the Champions League. At every match they boo the competition anthem, and the crowds at the Etihad for Champions League matches regularly fall well short of the numbers for domestic games.

When Guardiola arrived two years ago he seemed bemused by the issue, and spoke about it as though he assumed it would quickly go away.

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“I was not here for what happened but they must forget what happened in the past,” he said in September 2016. “Today the stadium is not completely full so the only thing we can do is play good so the people at home say, ‘wow, next time I will be there’.”

But Guardiola was wrong; the City fans did not want to move on, and were not ready to be won over by good football. By September 2017 he had changed tack, allowing that in a democracy “people can express what they want”, but continuing with his optimistic line that if the team played well, the fans would relent.

“What I want is to play good and the people who came here enjoyed our game,” he said after City’s 2-0 group stage win against Shakhtar. “Hopefully in the next games in the Champions League more people will watch us and support us because we need that in this competition.”

Instead the City fans’ disaffection seems to be getting worse. There were almost 15,000 empty seats at the Etihad last week as City became the first English side ever to lose four Champions League matches in a row with a 2-1 defeat to Lyon.

City had begun the game as though the indifferent mood in the stands had seeped into the attitude of the players, but they turned it around in the second half and going into the last 10 minutes they had pinned Lyon back and looked likely to get a late equaliser.

This is one of those situations in football when a passionate home crowd really can make a difference, mainly because of the flustering effect it can have on the opposition. But as Lyon’s players resisted the siege they must have taken heart from the sight of many City supporters moving towards the exits.

Might it be time for Guardiola to intervene in the situation with something a little stronger than "people can express what they want"? Remember that Jurgen Klopp had been at Liverpool for less than a month when he criticised his own supporters for leaving early as his players chased an equaliser against Crystal Palace. "Twelve minutes to go, I saw many people leaving. I felt very alone in this moment."

Mikel Arteta, who stood in for Guardiola at the post-Lyon press conference, was not so direct. "We have had this type of crowd in the Champions League before and we were able to win the game. If you ask me what is the ideal scenario, it is to have a full stadium every time, people supporting the team and being behind the team like crazy."

To Guardiola, who last appeared in a Champions League final seven years ago, and who desperately wants to win the competition again to prove that he can do so without Lionel Messi, the attitude of the City fans must feel like more of the stagnant, closed-minded insularity in which he has long considered that English football specialises.

Last season he took great satisfaction from the fact that his style of football could dominate in the English league, smashing the records for points, wins, and goals scored. Lest the significance of these achievements had gone over anyone’s head, Guardiola made sure to point it out at the time.

The truth is that he considers the Premier League to be overhyped and mediocre. During the recent international break, he told Jorge Valdano in an interview: "The Premier League looks better than what it is in reality. I'm surprised that despite having Messi, Cristiano, Barça and Madrid, the players and clubs who won the most trophies this last decade, La Liga couldn't reach that level. Maybe it's a marketing issue, I don't know."

Last Friday, answering questions from the press ahead of City's match against Cardiff – another facile 5-0 Premier League stroll – he explained City's defeat to Lyon in terms of the enormous step-up in quality between the Premier League and the Champions League.

“I insist many, many times it’s a completely different competition from the Premier League. The opponents ask a lot from us, it’s so demanding. The quality of them, the physicality – physicality is not just in the Premier League, in France they are physical too – and the quality of the opponents, it’s so hard in terms of the level of the teams.”

City fans might resent Uefa’s top competition but as far as Guardiola is concerned this is the only competition he really cares about. If the City supporters would like him to stick around they might want to start acting as though they care about it too.