A BBC Inside Out Yorkshire and Lincolnshire investigation into the 2017 failure of the Wakefield City Academies Trust (WCAT) reported that former CEO Mike Ramsay also ran a computer firm which supplied software to the trust's 21 schools.
According to the programme, to be screened on Monday, Mr Ramsay's firm made just over £840,000 during his time with WCAT.
Mr Ramsay's former office manager told the BBC how the CEO would claim 82p-a-mile mileage expenses as well as being paid £145 an hour for what he claimed were 16 or 17 hour days.
The investigation found that Mr Ramsay and his daughter made nearly £1 million from WCAT, which ran 21 schools before it collapsed.
The programme also said that two WCAT volunteer trustees, Steve Corne and Peter Mckenzie, were sacked after raising concerns about Mr Ramsey's remuneration and trust governance.
They said that, despite the trust running a £3 million deficit, Mr Ramsay wanted a huge pay rise.
Mr Mckenzie said: "Ramsay was challenged on this and he explained that he believed that by reducing the number of teaching staff he could address the budget deficit.
"I felt that this was completely fantastical and that it was impossible to remove enough teachers to address the budget deficit and carry on as an academy."
Former office manager Kirst Whipp told the programme that, while headteachers' pleas for funds were ignored, Mr Ramsay spent £1,500 on a pen for his dogs at his offices.
She said she was told to keep her boss's financial documents under lock and key and away from the finance team.
The programme said the 21 schools in WCAT lost £2 million between them in reserves.
One headteacher - Diane Humphreys of Waverley Primary School, in Doncaster - said: "It's clear to me that WCAT was run more like a business for profit."
She said: "Two hundred children were impacted because of the austere regime over that time impacting on their education, the resources, the money and the downward morale of staff."
Mr Ramsay categorically denied the allegations.
He told Inside Out: "I can confirm there was no conflict of interest, all connected party activity was in line with policy and scrutinised internally also by external audit and the ESFA (Educational and Skills Funding Agency) on a number of occasions, all of which is in the public domain."
He told the programme his expenses were submitted in line with policy and scrutinised by the chief financial officer.
Mr Ramsay told Inside Out that WCAT was allowed to expand too quickly without the resources to support the high number of schools needing improvement.
He said: "There were some inspirational people that worked for WCAT within the Central Team and Schools but, sadly, educational support was not enough or at the required level to make a difference."
The Department for Education told the BBC it had to pay £1.75 million in total to new academy trusts to take on the WCAT schools.
The department said it had taken steps to tighten accountability including requiring related party transactions over £20,000 to be approved by the DfE, high executive salaries to be justified and trusts being named if they do not provide the required financial returns.