In an emergency general meeting aimed at confirming Bayern's interim president Karl Hopfner as Hoeness's official successor, after the long-time club boss stepped down earlier this year, Hoeness said he would not go into hiding after his prison term.
"I made a huge mistake and I will accept the consequences for this," Hoeness told club members. "And then, when I return I will not go into any retirement. This wasn't it."
Hoeness, Germany's most famous soccer general manager, was convicted on March 16 of evading 28.5 million euros (£23.4 million) in taxes on income earned in a secret Swiss bank account and sentenced to prison in a spectacular case that grabbed headlines for months.
He had hoped his voluntary disclosure of income earned would lead to leniency and a suspended sentence but the Munich court convicted him to serve time in the Landsberg prison 70km west of Munich.
Hoeness said the German champions, whose hopes of retaining their European crown ended when they lost in the Champions League semi-finals to Real Madrid this week, would continue to be a dominant force in football even without him around.
"I am not concerned about the club at all," said Hoeness, who has overseen a sensational period of growth that has made Bayern one of the biggest clubs in the world.
"I am leaving with a good conscience. The club has no debts. The stadium is being paid off and the team won the league."
"If I had to paint a picture of this club I would have painted it exactly as it is now."
Hoeness was part of the successful Bayern team that won three consecutive European Cups in the 1970s before spending 30 years as a the club's general director. He was elected to the presidency in 2009, succeeding Franz Beckenbauer.
"I very much hope to see you all in good health when I return and this trauma is over," he said in an emotional speech before earning a minute's applause in Bayern's basketball hall where the meeting was held.
- Sports & Recreation