A reformed character: The renovation of St Giles' Cathedral

• One of the 6.2 million project's leading lights, the banker Sir Angus Grossart, and below, the restored interior. Pictures: Neil Hanna

'TIME has wrought its changes," wrote Robert Louis Stevenson in his 1879 Picturesque Notes on Edinburgh, "most notably around the precincts of St Giles". The High Kirk of Edinburgh had already seen its fair share of history by the time Stevenson started scribbling about it.

More than 700 years old by the 19th century, the Cathedral was undergoing another major restoration. Inside, the post-Reformation walls were being stripped back. Outside, a new sandstone exterior had been completed by the Victorians keen to preserve this icon of Scotland that is today known worldwide as the mother church of Presbyterianism.

Stevenson, however, wasn't blown away. "The church itself, if it were not for the spire, would be unrecognisable," he bemoaned. "The krames (an arcade of market stalls] are all gone, not a shop is left to shelter in its buttresses; and zealous magistrates and a misguided architect have shorn the design of manhood, and left it poor, naked, and pitifully pretentious."

Walking around the church with Sir Angus Grossart, you can't help wondering what Stevenson, whose bronze memorial is inside, would make of St Giles circa 2010. Thanks to another restoration, this one taking 16 years, St Giles is entering its next phase and the sombre Victorian feel of its interior has gone forever. Outside, the winking brass finials and vanes on top of the crown spire make the High Kirk look the very opposite of "poor" and "naked".

The St Giles' Cathedral Renewal Appeal aims to be completed next year when, on 26 January, a service of celebration is planned. So far 6.2 million has been spent on restoring the church, the money coming from the Heritage Lottery Fund, Historic Scotland and private donors including Grossart, the merchant banker, pillar of the arts in Scotland and chairman of the St Giles renewal campaign.

We meet outside the west-facing entrance on a suitably Victorian day: wintry, windy and thick with afternoon dark. Sir Angus stands at the top of the steps talking on his mobile, looking patrician and cold. He taps his umbrella against the wet steps.

"These are one of the newest parts of stonework," he says proudly. "Seven years old. Nothing has been done in a modest way. There is only one way to do a restoration of a building of this standard. Aren't these weathering well?"

St Giles is no stranger to change, turbulent or otherwise.

On 29 June 1559, John Knox famously preached the sermon in the High Kirk that ignited the Reformation across Scotland. He was appointed minister of St Giles the following year. Today, in the 450th anniversary year of the Reformation the latest restoration is drawing to a close. The building has regained some of the formal, understated grandeur of its pre-Reformation past. Even Kate Middleton's heart has been won over by this great grey icon of Scotland. She reportedly originally wanted to marry Prince William at St Giles, partly because they met in St Andrews.

"The important thing has been to keep the building in worship," says Sir Angus as we walk around Parliament Square. "No bride has been dusted with a cloud of stone. No organ recital has been interrupted with the sound of stone saws."

More than 200 craftspeople and contractors, the vast majority based in Scotland, have been involved in liberating the architecture of the building, doing expert work ranging from cleaning the 19th-century stained glass windows to installing the complex lighting system. Now the appeal is looking for a final 500,000 to realise the end of this project. "If you're going to have a national cathedral, as St Giles is, it should be at the highest international standard," says Sir Angus "Now you can actually see the latent beauty of the building which had to be unlocked. There has never been a chance to see it properly as an architectural whole. It's not just a church. It's not just a historic building. It's a place of unfolding beauty."

Sir Angus, who won't divulge how much he personally donated, walks us back up the High Street to get the best view of the medieval tower, the oldest part of the building, and the iconic crown spire. "The outsides of old Edinburgh churches," wrote Muriel Spark, "were of such dark stone, like presences almost the colour of the Castle rock, and were built so warningly with their upraised fingers." So the author of The Prime Of Miss Jean Brodie wrote when Edinburgh's most famous teacher asked her girls if they had visited St Giles.

Added in 1500, the crown spire is one of a few of this style from the period. (Another, in London, St Mary-le-Bow has long gone.) The tower housing a complex 12th century framework of oak timbers (which once held the church bells) has been reinforced, the masonry repointed and eroded stones replaced.

What you notice most are the gilded finials and wind vanes at the summit of the gothic pinnacles, each one designed to represent the Arts, the Law, Medicine and Parliament. Even in this dull weather, the brass glows in the gloaming. "We thought the decorative metalwork wouldn't have been there but when we looked more closely we realised it had," says Sir Angus. "The originals had disappeared for many years, probably at the time of the Reformation. I saw that tradition of decorative metalwork when I was looking at churches in Prague and Budapest."

It was a raging winter gale in 1979 that set St Giles on the path to restoration. The old weathercock roosting at the top of the spire began to sway madly and it became apparent that the structure of the old tower was no longer sound. Restoring the outer walls of the Kirk, replaced by the Victorians, would be no small task either. The sandstone shell had weathered badly, some stones had become soft and "sugary" and old iron fixings were rusting. It took 45 months to examine every single stone. "In the mid 19th century, St Giles was in a condition of severe decay," says Sir Angus as we step inside. "I've been up on the roof and there is a terrific amount of exposed stone and lead gutters. I took Prince Charles up there a few years ago. He was very interested in the crown spire and tower." Inside, the transformation is subtle but profound. We meet Danny Watson, beadle of St Giles, who jokes he heard we were coming and "stuck the heating on".

He scurries off to put on a light show that would put many stadium rock-outs to shame, taking us through each of the 20 "scenes". Some settings flood the vaults and the length of the nave and chancel with mellow light, others shroud far corners in darkness and make the space shrink and feel intimate. One setting makes the enormous German organ gifted 20 years ago light up like a rocket about to take off.

The chandeliers made locally in Dunfermline send light above and below, drawing the eye up to the medieval vault. Suddenly, what Sir Angus has been saying about liberating the building, making us see what is already there, makes absolute sense. "Before the lighting was installed, you wouldn't have picked any of this up," he says as once again we crane our necks and look up. His donation made the lighting scheme possible. "These things are wonderful punctuations of Renaissance architecture. And they were invisible. Now there is a sense of the eyes being cast upwards instead of being shrouded in gloom.

Before the pillars seemed to lead nowhere. And of course all this is the message of an uplifting spirit. It's not just about architecture."

At the eastern end of St Giles workmen are laying great slabs of English limestone, replacing sections of the old crumbling flagstones. Elsewhere the scaffolding is still up and amongst the hushed voices of tourists and worshippers there is the clatter of boots on boards, the sound of steel on stone, and a mobile phone ringing.

It's remarkable that so much work has gone on out of sight, the contractors huddled in the roof or disguising cable ducts as fake rainwater pipes. Two hundred wall monuments and sculptures have been restored. Two centuries worth of grime has been cleaned from marble, stone and alabaster. Mosaic floors have been tended, stained glass removed and cleaned with special solvents.

"All these monuments have been obscured in gloom and dirt," says Sir Angus, leading me into the baroque alabaster memorials honouring the royalist Marquis of Montrose and, on the other side, his nemesis Covenanter the Marquis of Argyll. "This is all part of the story of Scotland."

The Thistle Chapel hasn't been restored since it was built a century ago. "The oak woodwork was very dry so it was an elaborate job bringing it back to life," says Sir Angus. "Originally one of the Knights of the Thistle gifted it. It cost 24,000 a century ago, a huge amount of money but it still came in 80 under budget. There was a suggestion around the time that they would restore Holyrood Church beside the Palace. But it was so difficult and expensive that this chapel was commissioned instead."

Sir Angus first came to St Giles 40 years ago when he moved to Edinburgh from Lanarkshire. Like everyone walking past us or sitting quietly on one of the new chairs paid for by the congregation, whether they come to pray, brush up on Scottish history, or just appreciate the quiet splendour of the architecture, Sir Angus loves St Giles.

"It really is a beautiful and very refined building," he says, pointing his umbrella up to the vaults. "This cathedral took more than 100 years to build. We should remember that. In a thousand years of incredible history, the last 16 are nothing more than the blink of an eye."

• Visit www.stgilescathedral.org.uk/life/appeal for more information on the Renewal Appeal or email appeal@stgilesedinburgh to donate