The accusations facing Mark Houston of East Belfast Mission are reported to involve making false travel expenses.
He was removed from his post after a disciplinary panel met to discuss the claims which Mr Houston denies
EBM released a short statement to the BBC saying: "Mark Houston has been dismissed for gross misconduct, but this is now the subject of legal proceedings which will be heard in January.
"You will fully understand that EBM cannot therefore comment further at this time, as you will appreciate that we cannot say anything that might prejudice either party."
The charity works within its community offering all kinds of support from homeless services to employment and benefit advice, as well as a doubling up as a church.
The Department for Employment and Learning has confirmed a claim has been lodged with the Office of the Industrial Tribunals and the Fair Employment Tribunal.
Premier has contacted the charity and it's refused to comment any further.