Leaders say demand for 40,000 tickets to watch 41 performances of the £1.3 million production was weaker than expected. Approximately 65 per cent were sold.
Communications director Sharon Atkinson was quoted by The Times as saying: "There are lots of lessons that we will learn for the future."
The Mystery Plays lost nearly York Minster £590,000 last year however funds still rose by £2 million, owing in part to returns on investments and properties.
Sharon Atkinson went on to say: "We always knew that taking on the plays would come at a cost, but we took the decision to go ahead because of their importance to the city of York.
"We are not a commercial organisation. There is a Christian mission. One of those things is to get involved in lots of community initiatives."
York Minster acknowledged "a shorter run might have helped" and that concerns were raised over the length of each performance - four hours.
The Mystery Plays, which cover Creation right through to the Last Judgement, can be traced back to 14th century performances given at a time when most people could not read the Bible because it was written in Latin.