The Helensburgh building, completed in 1904, is considered to be the legendary Scottish architect’s domestic masterpiece.
It was placed inside the chainmail structure in 2019 as part of efforts to protect its saturated walls from further weather damage and to allow them to gradually dry out.
The NTS said £1.1m of new funding from the National Lottery Heritage Fund will allow it to replace the existing render on the property.
The conservation charity said that once the metal structure is removed, it plans to add updated permanent visitor facilities to the site, including a cafe, shop and toilets.
The package of funding, which is the first stage towards a wider £7.3m award, will support the charity’s Mackintosh Illuminated project, which aims to celebrate the genius of both Mackintosh and his wife Margaret Macdonald.
The funding announcement comes a year after the NTS acquired the Mackintosh at the Willow tearoom on Glasgow’s Sauchiehall Street.
The building, which was designed by the pair, had been struggling due to the impact of the pandemic and two fires at the Glasgow School of Art.
Philip Long, NTS chief executive, said: “We are enormously grateful to the National Lottery Heritage Fund for this generous grant which will help us do all we can to make sure that Mackintosh and Macdonald get the recognition globally and at home that their brilliant design and creativity merit.
“As the charity privileged to care for some of the finest remaining examples of the couple’s work, we feel strongly that their contribution should be better understood and celebrated.”
Mr Long added: “As a conservation charity, we will protect both buildings to be enjoyed and experienced long into the future.
“At the Hill House, this means continuing our work to solve its century-long issue with damp, both preserving this masterpiece and pioneering methods that add to the global conservation sector’s knowledge of how to care for and repair 20th century buildings, and helping train new craftspeople who can carry out work like this in the future.
“At the Mackintosh at the Willow, that means ensuring that this excellent experience thrives under the trust’s care and continues to grow and contribute to a much-needed revitalisation of Sauchiehall Street and to Glasgow’s heritage as a whole.”
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NTS said the project aims to raise the profile of Mackintosh and Macdonald both internationally and at home, through the creation of an online learning resource, and an expanded programme of property-based community and education work in both Helensburgh and Glasgow.
It also aims to encourage more people to visit both sites to get a richer picture of the pair’s skill and versatility.
Caroline Clark, heritage fund director for Scotland at the National Lottery, said: “Conserving the architectural masterpiece of the Hill House and enabling the NTS to tell the story of Charles Rennie Mackintosh and Margaret Macdonald’s creative collaboration is hugely important.
“Thanks to National Lottery players, the Hill House and the stunning Mackintosh at the Willow on Sauchiehall Street will together enable visitors to explore the work of these two artistic virtuosos whose influence stretches around the world.”
