Assistant head coach Dino Toppmoller will lead from the touchline when Bayern hosts Hoffenheim in the Bundesliga on Sunday (AEDT), having also stood in for the 4-0 win at Benfica in the UEFA Champions League on Thursday (AEDT).
Despite being fully vaccinated, Bayern's head coach Nagelsmann learned that the flu-like symptoms he was experiencing in Portugal were caused by COVID-19.
He said he feels "a bit weak" and is wary of getting in the way of the work being carried out by Toppmoller and fellow assistant Xaver Zembrod.
"Still, I am trying to take control if possible," he said.
"In isolation, I have built myself a little analysis centre with a big screen, iPad and laptop. I have different technical abilities now, also when it comes to the scouting feed for the game.
"It looks like a big data centre, right in my kitchen so that I have a short way to the tea kettle. I am positive that we will have a good impact. For training rhythm, this is not so bad because we don't really have training right now."
With such a heavy game schedule, Bayern's players are only ticking over between matches, rather than going through major sessions on the training pitch.
Nagelsmann is optimistic of being back at his Bayern desk in a matter of days, and says his positive test came as a jolt, insisting he had been trying to stay out of danger.
"I think we are all being cautious basically. This is hard, you cannot always say 100 per cent where you get the infection from," Nagelsmann said.
"I haven't done anything illegal or been at this party in Berlin where you had 22 people positive. I wasn't there, as an example. Basically, you never know. I was also a bit shocked.
"I just thought that I had a flu like many people at that time. For vaccinated people like me, things get less restricted and then you can also get infected easier.
"Of course, I went to a restaurant last week but I don't know ... I couldn't find out where I got it from. I don't think you can, this is really hard. The virus you have in your body doesn't come with a number that makes it trackable. That's just how it is."
Bayern heads into the weekend with a one-point advantage over Borussia Dortmund at the top of the Bundesliga, winning six and losing just one of its first eight games as it seeks a 10th consecutive league title.
Nagelsmann is in his first season with the club, having left RB Leipzig at the end of last season to take over from Hansi Flick, who left Bayern to become head coach of Germany.
Before Leipzig, Nagelsmann cut his teeth with Hoffenheim, so he misses out on a reunion on Sunday (AEDT).
Between 2016 and 2019, Nagelsmann managed Hoffenheim in 116 Bundesliga games, achieving a points-per-game average of 1.65, comfortably the best record of any coach of the club to have taken charge of at least five top-flight games.
Bayern will be looking to avoid a second successive home defeat in the Bundesliga on Sunday (AEDT), having been beaten 2-1 by Eintracht Frankfurt in its previous game at Allianz Arena. The previous time it lost consecutive league home games was in 2001 under Ottmar Hitzfeld.