In Ralph Agar’s map of Oxford, printed in 1578 and curiously portraying the south rather than the north of the city at the top of the map, a small church sits in open land to the north-east of the city centre.

Named Holywell Church, it was reached in the late 16th century by a brisk 15 minute walk from the centre of town, past Balliol College, along Canditch — the ditch outside the northern part of the city wall — the Ladies chapel and the wall of New College, until turning left onto Holywell Green, where the relatively isolated church sits close by Holywell House and a tiny hutch-like building a few feet away. This structure, as portrayed by Agar, is surely a covering known to have been erected over the Holy Well which gave the parish its name. Today that church is called St Cross and after many centuries as a place of worship, it is entering a new phase in its long existence. As Balliol College approaches its 750th anniversary in 2013, the college aims to bring its large and diverse collection of medieval manuscripts, early and rare printed books and more modern holdings of literary, scientific and political papers together in a Historic Collection Centre that allows the archive to be maintained in modern conditions and made accessible to students and scholars.

The collection will be housed in St Cross and will hold treasures indeed. Balliol has more than 400 medieval manuscripts, a surviving part of the college’s original library.

Central is the library of William Gray, Bishop of Ely, circa 1414-78. It has been described as ‘by far the finest, as well as the largest, private collection to survive in England from the Middle Ages’. More modern Balliol archives include the largest collection of poetic manuscripts by Robert Browning in the world, and the literary and personal papers of figures such as Matthew Arnold, Arthur Hugh Clough, Gerard Manley Hopkins and Algernon Swinburne — all Balliol men.

And there are the papers of Benjamin Jowett, the great and formidable Master of Balliol in the 19th century, including his long correspondence with Florence Nightingale (it is said that on being asked what she was like, he replied: ‘violent, very violent’). They corresponded for more than 30 years and the collection includes over 700 of his letters to her and some of hers to him. Also present are the Conroy, Morier and Jenkyns Papers (the latter a 19th century Master of Balliol who preceded Jowett); and from more recent times, the diary of Harold Nicolson and the papers of Lord Balogh.

Not content with all this, the college also has more than 15,000 pre-1800 printed books, many of them unique and thousands of title deeds dating from circa 1200, registers, estate maps, architectural drawings, correspondence and legal papers.

And this is where St Cross comes in, an ancient church which has been little used in recent times because of a steeply declining congregation.

It is situated next to Holywell Manor (formerly Holywell House), the graduate centre for Balliol.

The college has taken St Cross on through a 999-year lease, with an obligation to restore the fabric, including the painted ceilings and stained glass windows. Memorials and ancient features will be conserved and an environmentally controlled archive storage will be installed. There will be an exhibition and working space for researchers in the nave, while seminars and musical performances will take place from time to time — as well as the occasional religious service in the chancel. It is the fourth scheme of its kind in the city: St Peters-in-the-East is now the St Edmund Hall Library, All Saints Church is Lincoln College Library and St Luke’s, Cowley, is the Oxfordshire County Record Office.

It is certainly appropriate that St Cross should have been chosen and not just because of the historic connection of the church with Holywell Manor (the two buildings share a wall) and the opportunity to preserve one of the oldest buildings in Oxford. A college archive stretching back to around the 1200s will be housed in a church that has been in existence since around 1100.

The medieval Manor of Holywell was an agricultural area of some 250 acres and took its name from the nearby well. In its early years, St Cross was a chapel for St Peter-in-the-East, then the largest and most important church for the inhabitants of east Oxford within the city walls. Both passed into the ownership of Merton College in 1266.

The people of this parish, largely concentrated on Holywell Street, were baptised and buried in St Cross but paid their dues to the vicar of St Peter’s. But by the sixteenth century St Cross was largely treated as independent parish church.

St Cross was served almost exclusively by Fellows or other members of Merton. As with other Oxford churches and chapels, the style of service and ministry fluctuated over the years, but from 1849, St Cross had High Church curates, with an accompanying rise in congregation, helped greatly by the development of South Parks Road, Mansfield Road and Manor Road in the second half of the 19th century.

The number of Easter communicants rose from 145 in 1866 to 278 in 1887 and the Bishop of Oxford, the famous Samuel Wilberforce, warmly commended the state of the parish. Some parishioners though were less happy, protesting against ‘ritualistic practices’. Perhaps as a result of these grumbles, the Guild of the Holy Cross was formed to foster brotherhood among the parishioners and to counter any ‘sectarian spirit’. It met regularly until 1907.

In 1957 the benefice and the parish were re-united with St Peter’s and then joined to the university church, St Mary the Virgin in 1966. But the development of the parish in the 20th century, with the university and its colleges eroding the city population in Holywell, severely reduced the congregation and the ability of St Cross to continue as a functioning church.

So all parties, from the diocese of Oxford and St Mary’s to Balliol must be pleased that this ancient building will receive a new lease of life rather than a slow death.

The church itself stands on the east side of St Cross Road, and as Pevsner writes, ‘it still has the character of the village church next to the manor house’, even though it is now surrounded by modern university buildings such as the English and Law faculties.

It has an attractive, if slightly squat nave and chancel dating from the late 11th or early 12th century, the chancel arch surviving from a previous structure. North and south aisles were then added a century or so later, and a west tower in 1464. As with all buildings with a long history, there were many further additions and repairs: a south porch was built in 1592, the north wall rebuilt in 1685 and a vestry and organ chamber added to the north of the chancel in 1876. And the ancient and fine sundial was most recently renovated as a Millennium project. Inside the church, there are pleasing and varied monuments and brasses. The chancel and nave were restored as part of the works supervised by EP Warren in 1892-3. These works included the painting of an elaborate crucifixion by Reginald Hallward on the chancel arch. A nave ceiling was also painted: rows of IHS monograms amid foliage alternating with rows of suns. The east window stained glass is Victorian, by John Hardman, while the window at the east end of the south aisle was given in memory of Sir John Stainer, the Victorian composer and former churchwarden at St Cross. His grave is in the cemetery. Near the entrance door in the south aisle is a memorial to members of St Catherine’s College who fell in the two world wars. The college, designed by the Danish architect Arne Jacobsen and opened in 1964, is just down the road from St Cross but unusually for an Oxford college has no chapel — hence the memorial in the Holywell church.

There is also a war memorial to the dead of the parish of St Peter-in-the-East. And in a niche in the lady chapel is a Virgin and Child statue given in memory of Walter Pater and his two sisters, who are all buried in the cemetery. In the 18th and 19th centuries, Holywell Street nearby was home to prosperous Oxford businessmen and Aldermen, at least six of them becoming mayors of Oxford. Let John Knibb stand as their representative.

Born in 1650, he was twice mayor of Oxford, in 1698/9 and 1710/11. Famous locally as a clockmaker, with a business on the south side of Holywell Street, near The Broad, he became a freeman of the city, took on ten apprentices and with his wife Elizabeth had eight children between 1679 and 1694. All were baptised in the church, four were buried there also. Thomas Hearne, an Oxonian with an acid pen, says of Knibb: ‘this Nibb is a man of so little understanding that he was never known to laugh’. John Knibb died in 1722 and Hearne records: ‘1722 July 19. Last night about 8 o’clock, died suddenly Mr Alderman Knibb of Oxford, an old quite harmless man abt 4 score years of Age. He lived by Smith-Gate in Holywell parish (Smith-Gate was in Catte Street near the Octagonal Chapel). Tis said he eat his supper heartily, went round New Parks with his wife, sate himself down in his chair and died.’ He was buried inside St Cross, where on the north wall of the aisle is a fine memorial to him, his wife, their four dead children, their son Joseph’s wife and their son John and his wife.

But the most eye-catching and moving wall memorial, finely and sensitively engraved in brass, depicts Eliza Franklin, wife of the innkeeper of the King’s Arms, who died in childbirth in 1622. She is lying in bed, wearing a round hood cap with a deep frill, a cape and a gown with tight sleeves. On the bed covering are her four children, three of them in shrouds and one in swaddling clothes. Around the coverlet runs the legend: ‘of such are the kingdom of heaven’ And St Cross is not without literary associations. Alicia D’Anvers, daughter of Samuel Clarke, the first Controller of the Oxford University Press — who was also buried and commemorated in the church — wrote hard-hitting satirical poetry in the early 18th century and has a long and elegant Latin epitaph recording her many virtues.

There is a wall memorial to Rhoda Broughton, a successful novelist in at the turn of the last century, now unread, and the Inkling poet, Charles Williams was a regular member of the congregation.

But surely the best known literary association is described by Dorothy Sayers in Busman’s Holiday, when Harriet Vane marries Lord Peter Wimsey in the church.

The church had its final full service in October 2008. Let the last word go to the vicar, who said in his last sermon in the church of St Cross: ‘no one can easily halt demographic change. Here is an ancient village church now in the wrong place: no public transport, no residential population, no easy parking, little money to maintain a crumbling fabric, massive competition from college chapels and other city churches . . . it is greatly to the credit of those most committed to this place that they recognised that their Christian duty called them to seek redundancy for this building. It was painful, but right.’ And so a new age with Balliol begins.