Dairy farmer Sir Michael, 88, hosted the first festival on Worthy Farm, Somerset, in 1970 and was honoured for services to music and charity on Tuesday.
Speaking after the ceremony, which was presided over by the Princess Royal, the event's founder said both the King and Harry had attended the summer festival before.
Glastonbury has been held at Sir Michael Eavis' Worthy Farm, in Somerset, for more than 50 years. (AP PHOTO)
Sir Michael told the PA news agency: "The King came once, Prince Charles. And Harry - I think he jumped the fence I should think."
When asked how he knew this, Sir Michael chuckled and said: "I've got spies everywhere. No, I've got security all over the place actually."
He continued: "He enjoyed it!
"(The then) Prince Charles enjoyed it as well actually."
Regarding the duke's visit, the festival founder said: "He only came once. That was the old Prince Harry, before he went to America."
In 2013, Harry was spotted backstage watching The Rolling Stones headline the Pyramid Stage and partying until the early hours of the morning with Sir Michael.
Speaking at the festival that year, the dairy farmer said: "Prince Harry was great actually.
"I recommended that he should go on into the night, because the nightlife is what Glastonbury is all about.
"At three o'clock in the afternoon, you don't get it.
"I told him to get his taxi driver to come back at five o'clock in the morning and do you know what? He lasted until four in the morning.
"His friends were all having a great time. He didn't want to make a formal thing of being here."
Greenpeace, Oxfam and WaterAid all receive donations from the festival and the event aims to raise around two million pounds ($A3.8 million) per year, which also helps hundreds of local causes.
In 2023, the festival donated more than 3.7 million pounds ($A7.1 million) to a range of charitable causes and campaigns including homelessness organisation Centrepoint, food redistributors Fareshare, several refugee charities and mental health charity Mind.
Sir Michael said that more than three million people wanted to attend the festival this year, more than 50 years after the event was founded.
He said: "I'm so pleased that it became a success after all the grafting it took to get there.
"Trouble with the authorities and police and accountants and licensing and everything - in the end I had the last word!"
On his legacy and the future of Glastonbury, Sir Michael said he hoped the festival's organisation would remain "in the family" and called it the "best job in the world".
A representative for the Duke of Sussex was approached for comment.
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