Stone masons have begun work to repair the 15th century window - a painstaking project in which every pane must be individually removed and restored.
As one of the largest areas of medieval stained glass in Europe, the window could be worked on for up to 10 years.
The repair bill is expected to run into millions of pounds.
Huge area
Project leader Stephen Mills said: "A lot of that masonary at the top is actually 600-years-old so it has done very well indeed.
"It has fallen to us - our generation - to handle this massive project. It is very, very complicated."
Mr Mills said the stone masons would be starting at the top of the window, which covers 1,680 sq ft, and working their way down.
"The whole of the front will slowly be uncovered as the project carries on," he added, "so it will not be as you see it now for the whole eight to 10 years - if that's how long it takes."
The east window cost £58 when it was built between 1405 and 1408, paid by the then Bishop of Durham, Walter Skirlaw.
Ancient stained glass under wraps
York Minster's east window, regarded as one of the most celebrated pieces of stained glass in Europe, may be hidden by scaffolding for up to a decade.