Robert Mark Davies, 49, worked at Cyrenians Cymru, which offered a range of services to homeless and disadvantaged adults.
Mr Davies was arrested in 2014 following an investigation by South Wales Police's Economic Crime Unit.
He will appear at Cardiff Magistrates Court on 21 February accused of fraud by abuse of position.
The charity went into administration in February 2015.
The former head of finance at a homeless charity in Swansea has been charged with fraud.