Naz Malik, 65, denied swindling £15,000 from the now defunct All Wales Ethnic Minority Association (Awema).
He was cleared of one charge relating to a cheque for £2,500, and another of using charity funds to pay for a life insurance policy.
The Swansea jury could not reach a decision on a charge relating to a £9,340 cheque, and was discharged.
The Crown Prosecution Service (CPS) said it fully respected the jury's verdicts.
Catrin Evans, head of CPS Wales Complex Casework Unit, said: "With regard to the charge on which the jury were unable to reach a verdict, we will now take time to review the prosecution position before deciding whether or not to seek a retrial."
A former race equality charity boss has been cleared of two counts of fraud but a third charge is still outstanding.