Former Priory Federation chief executive Richard Gilliland, 64, was accused of misusing school credit cards to buy personal items and suppressing the results of a Criminal Records Bureau (CRB) check on his son.
The group's ex-finance director Stephen Davies, 58, faced three fraud charges.
The pair were found not guilty in a trial at Lincolnshire Crown Court.
The Priory Federation runs four schools in Lincoln and Grantham.
The trial previously heard Mr Gilliland bought items on school credit cards, including videos and condoms.
He said he was always owed money by the federation and used its credit cards to make his own purchases as "an off-setting exercise".
Mr Gilliland was also accused of suppressing the results of a CRB check so his son Kia Richardson - who had served a jail term for outraging public decency - could work at an equestrian centre run by the Priory.
He told the court colleagues were fully aware of his son's "troubled past".
Speaking after the trial, Mr Gilliland said: "It has been very hard to deal with, very emotional, but I am pleased with the result."
Mr Davies described the trial as "interesting", adding he was confident of the result as he had "done nothing wrong".
Two former senior members of staff at a Lincolnshire schools academy group have been cleared of fraud charges.