Eight-year-old Louise, who was seen last week accompanying her grandmother to an Easter service, now has her left arm in a cast.
She is being looked after at the family home in Bagshot Park by her mother Sophie, who cancelled a scheduled visit to a cancer hospital to be with her daughter.
Edward went ahead with the engagement, visiting the Christie in Withington, after learning his daughter hadn't been seriously injured.
A Buckingham Palace representative said on Thursday: "Lady Louise broke her left arm after falling from her pony while riding at Windsor this morning.
"She has been treated by doctors and is now resting at home.
"The Countess of Wessex was supposed to go to Manchester today with the Earl but understandably stayed with her daughter."
Lady Louise has inherited her grandmother's love of riding, and has been taught by the monarch and her groomers since she was little.
Though the Queen doesn't wear a helmet, she insists her grandchildren are properly protected while riding – and it's understood Louise was wearing a hard hat and back brace when the accident happened.
The little girl, who is ninth in-line to the throne, is a regular visitor at Windsor Castle's royal mews, where her pony is stabled.
Louise, who has a younger brother – four-year-old James,Viscount Severn – is largely kept out of the spotlight by her parents, but has increasingly been in the public eye since the duke and Duchess of Cambridge's wedding last year.
She suffers from extropia, a rare eye condition that has left her with a slight squint.
It is thought that she has had surgery to correct it, but may require more.