Nick Mwendwa has stepped aside as president of Football Kenya Federation (FKF) after being charged with multiple counts of fraud.
In a letter to FKF's national executive committee members, Mwendwa stated he was handing over the reins to vice president Doris Petra because he felt "personally targeted" by his arrest and the subsequent charges, which he denies.
"In light of the frequent arrests and detentions, which have adversely affected my family and personal business, and whilst I am confident I will be cleared of any wrong doing in the end, I have asked my vice president Madam Doris Petra to assume all functions of the FKF president," Mwendwa wrote.
"My decision has been arrived at with the federation's best interest at heart."
On Monday Mwendwa pleaded not guilty to four counts of fraud at an anti-corruption court in Nairobi, having been re-arrested by police on Friday.
The total amount of money Mwendwa and others, who were not present in court, are accused of taking from FKF is about 38m Kenyan shillings ($337,700, £254,500).
Mwendwa, who had been head of the FKF since 2016, is currently out on a cash bail of 10m Kenyan shillings as he awaits trial.
Among the terms of his bail, Mwendwa has been instructed to deposit his passport with the court and is forbidden from accessing FKF offices.
This week's court appearances come a fortnight after Mwendwa was released on bail after a previous arrest.
Last Thursday the FKF announced the case against him was over and the court returned his cash bail of 4m Kenyan shillings - but the Kenyan police later clarified that it was not the fraud case which had been closed.
It meant that the country's Directorate of Criminal Investigations (DCI) continued its investigations and eventually arrested him for a second time, with Mwendwa then being formally charged with corruption.