Robert Davies used to work as head of finance for Swansea-based Cyrenians Cymru, where 20 staff lost their jobs.
The 49-year old pleaded guilty to one count of fraud by abuse of position at Cardiff Crown Court.
The charge relates to the six-year period between June 4, 2008, and November 11, 2014, and involves £1,343,074.
Davies was arrested in December 2014 on suspicion of “extensive fraud”.
He previously appeared in Cardiff Magistrates’ Court on February 21 where his case was sent to the Crown Court.
The defendant then appeared before Judge Philip Harris-Jenkins at Cardiff Crown Court on March 21 but did not enter pleas.
The malpractice came to light following an investigation by the South Wales Police Economic Crime Unit.
Speaking at the time of Davies’ arrest in 2014, the charity’s chief executive Conrad Watkins said the staff were “all distraught” by the investigation.
Mr Watkins said the board of trustees and senior management instigated an independent financial investigation.
He said the investigation revealed issues that were reported to the police.
Since the investigation Cyrenians Cymru was forced to declare itself insolvent and went into administration in February 2015, with 20 jobs affected.
The charity was set up in 1973 to tackle homelessness and poverty in Swansea and the wider west Wales area.
He was remanded in custody until he is sentenced on April 25.
There will be a hearing under the Proceeds of Crime Act.