It was a shock but also a logical end point, the surprise that you knew could be coming. Although a visibly stunned Thomas Müller insisted after full time on Tuesday that “an [equalising] goal wasn’t in the air”, Samuel Chukwueze’s late goal for Villarreal that ousted Bayern Munich from the Champions League was a sucker punch via a predictable route.

Although on paper Bayern had breezed past Red Bull Salzburg in the previous round, they had diced with danger – Kingsley Coman equalising late in the first leg after Salzburg had worn themselves out. Matthias Jaissle’s young team even had the better chances early in the Allianz Arena return before shooting themselves in the foot defensively. Unai Emery’s Villarreal had the experience and sang-froid that the Austrian champions hadn’t. Domestically in recent weeks, Bayern have offered Borussia Dortmund routes back into the Bundesliga title race that Marco Rose’s side haven’t been good enough to take.

Part of the issue has been Julian Nagelsmann’s stubbornness. Bayern have played some undeniably fantastic football under him this season but they have often looked careless – and given the sheer recklessness of some of the team’s play under his predecessor, Hansi Flick, that’s saying something. It has felt for some time that they have been playing with one attacking midfielder too many, although that has been partly to do with the four-month absence of the recently returned Leon Goretzka, and Nagelsmann has not seen fit to change. “I’ve been asked the question 1,734 times in the last few weeks,” he said after last month’s draw at Hoffenheim. When it mattered, his team were too easy to cut through, while lacking attacking fluency with Leroy Sané and Serge Gnabry not in their best form.

Whether Nagelsmann has the squad to change tack between games is the question. Personnel is the main issue, and the main mitigating factor for the coach. “Better challengers must be added” to the first XI players, wrote Kicker’s Karlheinz Wild on Wednesday. “It’s going to be a difficult job. Finance dictates unwelcome constraints … and imagination is required for structural reforms.” Improving the squad is one thing. Doing it when Robert Lewandowski, Manuel Neuer, Müller and Gnabry are out of contract in 2023 is even trickier.

Bayern’s manager, Julian Nagelsmann, with Serge Gnabry, whose departure would be a big blow.
Bayern’s manager, Julian Nagelsmann, with Serge Gnabry, whose departure would be a big blow. Photograph: Markus Gilliar/Getty Images

Losing Gnabry, the present and the future at 26, is unthinkable. The issue, though – which bleeds into the other potential renewals for the experienced cornerstones of the team – is that it will cost Bayern, particularly in the wake of Coman signing a new deal in January estimated to pay him €17m a year, before bonuses. The scenario of Bayern coughing up for all of Gnabry, Neuer, Müller and Lewandowski is difficult to envisage.

It’s the policy that led to Niklas Süle signing for Borussia Dortmund from this summer – much to Nagelsmann’s displeasure – and has always been thus at Bayern, with that willingness to set limits prompting the exits of Toni Kroos and David Alaba in the past, for example. You can’t pay everybody what they want. That means some tough choices await and the work of Hasan Salihamidzic, who has never universally convinced as sporting director and frequently clashed with Flick on squad planning, will be under scrutiny too.

There is a need, as Nagelsmann has agreed with the club’s decision-makers, for a big defensive restructure. Dayot Upamecano, who gave another shaky performance in the return against Villarreal, is taking time to settle, and it is legitimate to ask whether Lucas Hernandez and Benjamin Pavard have truly justified their significant transfer fees (the former remains, by some distance, Bayern’s record signing at €80m). The departures of Alaba and Jérôme Boateng last summer stripped the defence of a great deal of experience and Nagelsmann has been juggling expectations while dealing with that.

Lucas Hernandez, battling here with Villarreal’s Francis Coquelin, has not justified his €80m fee.
Lucas Hernandez, battling here with Villarreal’s Francis Coquelin, has not justified his €80m fee. Photograph: Eurasia Sport Images/Getty Images

This is the first major test of Oliver Kahn since he was elevated to the position of CEO. Bayern are so associated with strength and continuity off the pitch that it has been easy for the rest of Europe not to notice the profound changes in the club’s boardroom. Kahn will be expected to act decisively to move on from the disappointment – although Nagelsmann, a long-term project for the club, is likely to be safe. As Süddeutsche Zeitung’s Philipp Selldorf pointed out on Wednesday, the former powerbrokers Uli Hoeness, and Karl-Heinz Rummenigge “will be listening carefully” to Kahn’s forthcoming public statement.

“We lost it in the first leg,” said Nagelsmann on Tuesday night. Bayern’s inability to react to that setback means they must move quickly to retain their place among Europe’s elite.