In the city of ‘dreaming spires’, the University Church of St Mary the Virgin can claim the tallest and finest of them all. First recorded in the Domesday Book in 1086, the famous church on the High can also claim to be the first home of the university itself, as opposed to any of the halls and colleges. And with 300,000 visitors a year — a figure amounting to almost twice the city’s population — there cannot be many churches in England with more people passing through its doors.

Yet this jewel in Oxford’s architectural crown has seen little major restoration work down the centuries. The 13th-century tower saw some repair work in the 17th, 18th and 19th century, with restoration work carried out under the direction of Sir George Gilbert Scott in the 1850s and later by another great Victorian figure T.G. Jackson, while the Vaults Cafe was opened in the Congregation House in 1990s.

Yet none of this compares in scale with the work that is now being undertaken at the Grade I listed church thanks to a £3.4m Heritage Lottery grant.

The first scaffolding went up last week to mark the beginning of an 18-month project to repair the church’s facade, stonework, spire and tower as well as vital repairs to the interior. St Mary’s Vicar, the Rev Canon Brian Mountford, said: “This project is the culmination of five years of planning to secure a programme of renovations and improvements to St Mary’s.

“The next year will be challenging but it is very exciting to see the works finally commencing, and I know the end result is going to be magnificent.”

But he believes the project is about far more than restoration and conservation. “To begin with it means we must conserve and protect the outstanding heritage of the building, including the iconic tower and spire. But then we need to unlock and make accessible our heritage which so many people come here to discover.”

The history of the church will be more effectively displayed, with plans for an interpretations scheme and heritage education and volunteering programmes, with up to 200 local people being offered the chance to train as guides. The work, however, in the coming months will see one of the city’s great landmarks disappearing behind scaffolding, to the disappointment of thousands of visitors to the city.

Sophie Slade, project co-ordinator, said: “It is going to take until the end of the year just to get all the scaffolding up, with work then expected to start in January. The first phase of the scheme, involving scaffolding on the tower and north east corner of the site, is really just enabling work. But it will be the most complicated and the most disruptive. Putting the scaffolding up is made more difficult because the tower is on the side of the church. Sadly, the scaffolding will be up until June. The tower will be closing within the next two weeks and is unlikely to reopen before the end of May. In January, works to the tower, library, cafe, shop and chancel will begin, with most of the church closed and access limited to the nave and offices.”

The university built the Congregation House and Library as its first dedicated building in the 1320s — and this part of the church is to receive particular attention with refurbishments to increase public access to the first floor and tower levels. A new lift up to the first floor is being added. along with a new public toilet, positioned near the staircase leading to the tower. The entrance to the Old Library houses one of the most historic parts of the building. A screen encased in a wall is believed to be the former choir screen from the pre-16th church. So this wall will be opened up, with restoration work allowing visitors to see into the library when it is not in use.

Another original feature that will be restored is an oval window in the north wall, to create one of the best views of Radcliffe Square and the Camera. The De Brome Chapel, dating from 1328 on the west side of the tower, will become the focal point for visitors beginning a tour of St Mary’s and a new entrance will be created from an existing blocked-up doorway. Next year the church will be launching a competition to design a new stained glass above the new entrance, which should focus on the early years of Oxford University at St Mary’s.

Phase three of the work will involve a partial hand-over of some areas of the church, before a final phase, which will focus on the nave.

The total cost of the work is likely to exceed £5.5m, with a development fundraising campaign launched and major support coming from Oxford University and the Clore Duffield Foundation.

The first major restoration since 1896 of St Mary’s — built with stones quarried from Headington Hill — will be undertaken by Cambridge firm Caroe Architecture, a young company only established two years ago.

Oliver Caroe, principal of the company, said: “Our task will be to work with the church team to engage the mind, eyes and ears of the visitors from many communities and backgrounds. Our goal is to provide a sensory experience that will trigger a transformative encounter.”

When he announced the big Lottery grant earlier this year, the head of the Heritage Lottery Fund Stuart McLeod described it as “an inspirational and important project showcasing our heritage at its very best, by providing a special look into the past”.

When it comes to giant personalities of the past, St Mary’s is almost unrivalled. Archbishop of Canterbury Thomas Cranmer was tried in the church, the Oxford Movement and Oxfam were founded here, and the voices of such distinguished preachers as the Wesley Brothers, the Blessed Henry Newman and C.S. Lewis have echoed around its walls.

Soon it will echo to the sound of workmen. But the end product should see St Mary’s through the next 50 years and beyond.