Hannah Ingram-Moore and her husband, Colin, were ordered to get rid of the complex by Wednesday.
The couple had been granted permission to build the 'Captain Tom Foundation Building' at their £1.2 million home in Marston Moretaine, a village in Bedfordshire, in the east of England.
Instead of the foundation building, they built a much larger structure - which has now been demolished.
The process of demolition included the removal of roof tiles, one at a time, and moving out gym equipment and awards.
Over the weekend, a gaping hole was left in the ground of the spa complex after a crane removed the swimming pool.
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Previously mementos such as Captain Tom's Sports Personality of the Year award and Guinness Book of Records certificate were seen being taken out of the building.
Captain Tom's family lost an appeal against Central Bedfordshire Council to keep their spa complex after a planning inspector ruled it was 'at odds' with their Grade ll listed home in Marston Moretaine.
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The council issued an enforcement notice last July to demolish the unauthorised building and their appeal was dismissed last November.
They were given three months to remove the sauna and spa and it must be pulled down by February 7.
Captain Tom raised almost £39 million for NHS charities by walking around his garden 100 times using a walking frame during the first Covid lockdown in the spring of 2020. He was later knighted by the Queen and died in February 2021.
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Last week one local, whose home overlooks the spa, said: "It is a humiliation for Hannah. I think she thought she could get away with it. I wonder if they will move when it is all over."
The foundation is the subject of an investigation by the Charity Commission amid concerns its management and independence from Sir Tom's family.