The Spaniard, who is currently on a year-long sabbatical, will take the reins from Jupp Heynckes at the end of the season, but Kahn has said that it does not necessarily mean instant success for the Bavarian outfit.
"Guardiola brought up players from youth to professional levels, but Bayern's players need not possess the same level of automatism as Barcelona's do," Kahn wrote in German newspaper Bild.
"To internalise his systems will not happen in one day. Unlike Louis van Gaal's single-minded usage of the ball to achieve an end result, Guardiola's system is more flexible, with possession central to play.
"Guardiola and sports director Matthias Sammer must develop and implement a consistent philosophy. Doing so will be a decisive factor in the battle to be Europe's number one team."
Guardiola won 14 trophies during his four years coaching Barcelona.