Meghan, the Duchess of Sussex, and Prince Harry were originally paying back the money in monthly instalments. But a spokesman for the Sussexes has confirmed the cash will be paid in full to the Sovereign Grant.
The Duke and Duchess of Sussex stepped down as senior members of the Royal Family earlier this year.
The Sussexes were previously paying back the money for Frogmore cottage at £18,000 a month which also covered rent for the property.
It would have taken the Duke and Duchess 11 years to pay back the taxpayers’ money if they had continued paying the monthly instalments.
But a spokesman for the Sussexes announced they will be repaying the money in full.
He also said the Sussexes will be continuing to use Frogmore Cottage as a UK base.
He said: “A contribution has been made to the Sovereign Grant by the Duke of Sussex.
“This contribution as originally offered by Prince Harry has fully covered the necessary renovation costs of Frogmore Cottage, a property of Her Majesty the Queen, and will remain the UK residence of the Duke and his family.”
The spokesman announced they will pay an undisclosed “commercial” rent for the Windsor property.
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Since the couple stepped down as senior royals, the £2.4million of taxpayers’ money has been a controversial topic.
The debate was heightened after the Sussexes reportedly bought a mansion worth £11million in Montecito, Santa Barbara.
The couple are believed to have bought the nine-bedroom, 16-bathroom property with a £7.5million mortgage.
The couple also recently signed a multi-year deal with Netflix to produce TV series, documentaries and children’s shows.
The deal with the online streaming giant is said to be worth about $100million.
The source said the news of the Sussexes’ repayment had come as a surprise.
They said: “This has come as something of a surprise, and it can only be assumed this has something to do with the Netflix deal.
“Maybe it now means he can afford to pay the money back in full at once or maybe he has been irritated by the criticism that the deal has led to of his finances. No one really knows.
“But if he thinks that it will make him immune from public and media scrutiny, he is misguided.
“This new, highly visible media role that he is seeking in the US makes him more of a public figure than ever.”