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".

Only 13 of the 1948 Gandhi 10-rupee Purple Brown and Lake 'Service' stamps are in circulation.
The block of four was sold to a private collector-investor in Australia for the highest ever price for Indian stamps, said dealer Stanley Gibbons.
However, the record price for a stamp sold an auction was $9.5m (£7.4m).
That British Guiana one-cent magenta stamp was sold to an anonymous bidder in June 2014.
The Indian stamps were particularly rare owing to the fact they were in a set of four.
Stanley Gibbons previously sold one of these singles for £160,000 to a client in Uruguay last year.
A block of four is in the Queen's stamp collection, which is believed to be the world's largest and most valuable in private hands.
Keith Heddle, managing director of investments at Stanley Gibbons, said: "The market for high-quality Indian rarities has been strong for several years and is supported by the ongoing desire of the wealthy Indian diaspora and savvy international clients to own these historic assets."

His villainous character Ethan Rayne was the arch enemy of regular character Giles, played by Anthony Head.
The London-born actor also played the evil General Sarris opposite Tim Allen in Galaxy Quest.
His ex-wife Casey Defranco called him "a wonderful person, extraordinarily talented as an actor."
Staff on his official website wrote: "Please join us in raising a glass to Robin - goodbye, dear friend. Thank you for all the laughter and the cookies. We will miss you so very much."
Sachs' first role was with the British Hammer film studio, in the movie Vampire Circus.
He went on to play Adam Carrington in the 1991 miniseries Dynasty: The Reunion when the original actor Gordon Thomson was unavailable.
Sachs worked on several sci-fi shows, with appearances in Babylon 5, Star Trek: Voyager and Torchwood: Miracle Day.
His stage work included touring productions of Hamlet and Twelfth Night.
In 1999, he appeared heavily disguised under layers of heavy make-up as the baddie Sarris in the satirical comedy Galaxy Quest, which co-starred Sigourney Weaver and Alan Rickman.
Later in his career, Sachs provided voices for several video games including Mass Effect 2 and 3 and Resident Evil Damnation.
Two former senior members of staff at a Lincolnshire schools academy group have been cleared of fraud charges.
[NEXT_CONCEPT]
A set of four stamps featuring the portrait of Gandhi has been sold for £500,000 - but the total remains well short of an international record.
[NEXT_CONCEPT]
British actor Robin Sachs, best known for his role in the hit TV series Buffy The Vampire Slayer, has died at the age of 61.