The repayment includes about €24m (£21m) in income tax and almost €25m (£22m) in fines for what authorities had described as a “very serious” infringement.
The tax agency said it would appeal to the Supreme Court and that no payment would be made until the final ruling.
Shakira lived with former Barcelona and Spain footballer Gerard Pique for more than a decade after reportedly meeting in 2010 while filming the music video for Waka Waka, the official song of the World Cup in South Africa.
The High Court said the fines were unlawful because they relied on the assumption that Spain was her tax residence for the 2011 fiscal year, “a fact which has not been proven”.
The court said the singer spent 163 days in Spain in that financial year – 20 days short of the threshold for her to be classed as a resident for tax purposes.
The case does not involve the tax years after 2011.
It was one of several cases involving Shakira to have been brought by Spain’s tax agency.
In 2023, she reached a deal with Spanish prosecutors to settle a separate tax fraud case covering the years 2012-2014, just as she was set to go on trial.
The deal meant Shakira, who denied any wrongdoing, accepted six charges and paid a €7.5m (£6.5m) fine.
Prosecutors had wanted to jail her for eight years and fine her €23.8m (£20.8m) if she was found guilty. She said she settled the case “with the best interest of my kids at heart”.
And in 2024, a Spanish court reportedly, external dropped an investigation into her tax payments for 2018 because of “a lack of evidence”.
