The Bavarians’ title was confirmed following Bayer Leverkusen’s inability to defeat Freiburg during the weekend.
While the former Germany international praised Bayern’s title triumph, he criticized the club’s leadership for poor transfer choices.
"Overall, the season was only satisfactory in my opinion, because their performance in the cup competitions was too low," Matthaus wrote in a column for Sky Sport.
"Max Eberl fares worse than the coach. Michael Olise was a very good signing, but not all of his transfers have worked out. Eberl's assessment is not only about his sporting performance, but also about how he represents the club externally as sporting director.
"His statements about Leroy Sane on Saturday and Thomas Muller in January caused considerable confusion externally and unrest within the club."
Matthaus added: "Serge Gnabry and Kingsley Coman have also been with the club for a long time, and both are injury-prone. The attack would benefit from a breath of fresh air.
"A breath of fresh air like the one Olise has brought, who, at 21, is already performing well and still has potential for improvement.
"Bayern has the strongest squad in the Bundesliga, but they are missing a second penalty box player behind Harry Kane in attack - and a lot of things have not worked out in defense either."