When she knighted him she personally recognised his achievement, saying, "Thank you so much, an amazing amount of money you raised".
After the announcement of his death, Buckingham Palace said: "The Queen is sending a private message of condolence to the family of Captain Sir Tom Moore. Her Majesty very much enjoyed meeting [him] and his family at Windsor last year.
"Her thoughts, and those of the royal family, are with them, recognising the inspiration he provided for the whole nation and others across the world."
Over the weekend, Captain Tom's daughters Hannah and Lucy said he had been diagnosed with Covid-19 last week.
He'd also contracted pneumonia this month, meaning he wasn't able to get a Covid vaccine.
"It is with great sadness that we announce the death of our dear father, Captain Sir Tom Moore," his daughters wrote.
"We are so grateful that we were with him during the last hours of his life; Hannah, Benjie and Georgia by his bedside and Lucy on FaceTime.
"We spent hours chatting to him, reminiscing about our childhood and our wonderful mother. We shared laughter and tears together.
"The last year of our father's life was nothing short of remarkable. He was rejuvenated and experienced things he'd only ever dreamed of."