At Bayern Munich Pep Guardiola has shown tactical acuity and attention to detail without equal, but has fallen out with anyone who has whispered a complaint

The occasion was mundane, the opposition mediocre. But you wouldn’t have known either from the enormous, coffee table-sized dossier Pep Guardiola was carrying through the corridors of Bayern Munich’s Säbener Strasse headquarters before October’s home game against Cologne, the sort of game his club – the unassailable leaders, who had walked all nine of their Bundesliga matches at that point – were expected to win at a canter.

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The manager locked himself in his office to study videos of the mid-table team for hours on end and emerged the next day to provide his side with a detailed analysis of where space could be found.

Cologne made life difficult with a five-man defence and 10 men behind the ball at the Allianz Arena. But spaces began to open up in precisely in the areas Guardiola had mapped out in the team meeting.

Bayern took full advantage to destroy the visitors 4-0, leaving one long-serving member of the coaching staff shaking his head on the sideline, a disbelieving grin on his face. “Pep, he’s a genius,” the same club employee said two months later as he described that example of Guardiola’s attention to detail.

There are countless similar anecdotes that tell of the 44-year-old’s professional dedication since pitching up in the Bavarian capital in the summer of 2013. Talk to any of the former greats on the Bayern board or even to employees who can view the senior team’s training pitch from their canteen, and they all, to a man, volunteer that they have never seen a manager as brilliant as Guardiola at work.

Facebook Twitter Pinterest ‘Regular employees who can view the senior team’s training pitch from their canteen all, to a man, volunteer that they have never seen a manager as brilliant at Guardiola at work.’ Photograph: Michaela Rehle/Reuters

Practice sessions are varied and intense, team talks nothing short of enlightening. Another influential Bayern official not prone to exaggeration told the Observer that “Guardiola thinks about football and understands the machinations of the game at a level so deep that no one can follow”.

The midfielder Toni Kroos worked under Jürgen Klinsmann, Louis van Gaal, Jupp Heynckes, Carlo Ancelotti and Rafael Benítez, but he, too, recently said that Guardiola, his manager at Bayern in 2013-14, “was the best coach I ever had in terms of his football ideas, his plans for playing against sides and presenting solutions to his own team”.

A Champions League trophy has eluded the Spaniard in Munich but the club have been extremely pleased with the team’s development into football’s equivalent of the Terminator II model: they can shift shape at will, adapt to any situation and take down their opponents in a myriad ways.

The constant tactical demands on his players, overbearing at first, and a remarkable work rate without the ball have resulted in many of them reaching levels not seen before. David Alaba has grown into one of the world’s most accomplished all-rounders on Guardiola’s watch, defender Jérôme Boateng sprays 60m pinpoint passes and roving forward Thomas Müller now commands a nine-figure price tag.

That’s the “genius” bit covered. For all his charming, approachable demeanour outside the stadium, Guardiola has proved more high-maintenance and difficult to work with than anticipated. He still has not come to terms with a corporate culture that sees key figures frequently engage in robust exchanges of views. In turn, Bayern do not understand why he has often sent assistants or advisers to raise important issues with the board, instead of talking to them directly. The lack of open communication has bred mistrust on both sides, especially since the summer’s tour of China.

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The otherwise successful trip ended on a very frosty note when the club chairman, Karl-Heinz Rummenigge, innocuously remarked that life at Bayern would continue even if the manager did not renew his existing contract beyond June 2016. Guardiola took huge offence and sulked throughout the flight home to Germany.

He was also upset that the Bayern president, Franz Beckenbauer, criticised the team’s play as over-elaborate in the wake of their humiliating Champions League semi-final defeat by Real Madrid in 2014. Confidants explained he felt his footballing ideals were gravely misunderstood in Munich.

There were endless rows with Bayern’s club doctor, Hans-Wilhelm Müller-Wohlfahrt, over players’ recurring injuries. The 73-year-old resigned in protest after nearly four decades at the club in April – Rummenigge had taken Guardiola’s side in their long-running dispute – but Kicker reported on Thursday that Müller-Wohlfahrt’s successor, Dr Volker Braun, has also fallen out with Guardiola over the latest setback for Franck Ribéry. The Frenchman will miss the next eight weeks with a muscle tear.

Facebook Twitter Pinterest Kicker have reported that Pep Guardiola has fallen out with Bayern Munich’s club docter, Volker Braun, over Franck Ribéry’s latest injury. Photograph: Alex Grimm/Bongarts/Getty Images

Some of the coaching staff and a few of the German contingent have privately expressed reservations about the manager forsaking traditional fitness drills for exercises with the ball. It could well be a simple question of habit: they are not used to working that way. Some players have done extra sessions in their own time to make up for the perceived deficit, which might well have proved counter-productive. In the past two seasons Bayern’s performance levels have dropped a little after the winter break and injuries have piled up.

As much as Guardiola’s exacting methods and complex personality have exhausted the club, Bayern would still have been prepared to overlook it all to tie him down for a few more years. Such has been the impression he has made in pure footballing terms. But he has got other plans. Sources close to Guardiola insist that he always intended to leave at the end of his contract, that there are no specific reasons why he has turned down a new deal.

Now that the game’s most in-demand coach is about to announce his departure at the end of the season, Bayern are hopeful that his three-year stint can still deliver a happy ending. When the Bavarians revealed that Guardiola would take over from Heynckes, in January 2013, players and the incumbent coach were galvanised to deliver the treble five months later. Maybe history can repeat itself.