Director of music Robert Sharpe will play the historic instrument for the live-streamed worship, which will also include a blessing ceremony, and the Grand Organ is expected to play a full part in Lent this year, leading up to its dedication at Easter.
It has been out of public sight since 2018, when a 'once-in-a-century' £2million restoration project began under the guidance of specialist contractors Harrison and Harrison.
They were entrusted to coax one of the country's oldest ecclesiastical organs back into life, overseeing a painstaking process known as 'voicing' which takes place just once in every generation and revitalising 5,400 pipes.
Voicing has similarities to piano tuning, but it alters the tone and volume of each pipe as well as the pitch.
The onerous task had to be done entirely manually by 'voicer' Andrew Scott, who listened to each pipe's individual note.
He is the first person to undertake the job since 1903, when the Grand Organ underwent its last major refurbishment.
The Minster's own mason conservators were also involved in an associated project to clean the Pulpitum, a 15th-century stone screen which separates the Quire from the Nave. It features intricate carvings of medieval monarchs, and special vacuum cleaners have to be used to remove years' worth of dirt and dusk. The screen was revealed again last autumn after spending two years encased in scaffolding.
York Minster s Canon Precentor Vicky Johnson admitted that the first recital would be a 'bittersweet' moment in the absence of a large audience.
"Ideally, we would want the Minster to be full of people singing hymns, but it is still a great joy to have the organ back and it's a step along the way. It will be a low-key revealing, but Lent is solemn in tone and the Archibishop will dedicate it on Easter Day."
The restoration threw up a few surprises, including a lost hymn book from the 1980s discovered at the bottom of a pipe and 30 pipes which were found to be beyond repair.
"It's gone really well, and it's been such an inspiring, innovative project. A lot of thought goes into this kind of instrument - it is so intricate and beautiful, and it is easy to take it for granted."
Director of music Robert Sharpe added: "The refurbishment preserves the unique sound of the Minster’s organ whilst renewing its mechanism. Work has included bringing many of the 102 case pipes which have been silent since 1903 back into use and restoring the grander, imposing qualities of the instrument which were altered during work in the 1960s.
“Organ music has played a central role in worship at York Minster for nearly 1,000 years and we hope this project will help ensure that tradition continues throughout the 21st century and beyond.”