Charles and Camilla looked sombre as they entered the church in Derbyshire just behind the hearse and the Duke of Devonshire.
The pair were amongst the hundreds of mourners who gathered to celebrate the life of the 94-year-old woman, who was the last of the famous Mitford sisters.
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Around 200 guests packed into the church but hundreds more crowded outside to follow the funeral on two giant screens.
Canon Dave Perkins led the service, which began with the hymn Holy, Holy, Holy, and the Dowager Duchess was later laid to rest in the Cavendish family plot.
The Duchess lived at Chatsworth House in Derbyshire, and the garden of the estate will be open all afternoon for a celebration of her life, following the Duchess's express wishes that no memorial service was held.
As the hearse left the estate on Thursday morning for the church, 600 of the estate's staff lined the route to pay their respects.
Charles and Deborah were close friends, and when the Duchess died last month at the age of 94, Charles issued a personal tribute, in which he spoke of his and the Duchess of Cornwall's "deep sadness".
"We shall miss her so very much," he said, describing her as a character who "will not easily be forgotten".
He continued: "She was a unique personality with a wonderfully original approach to life, and a memorable turn of phrase to match that originality.
"The joy, pleasure and amusement she gave to so many, particularly through her books, as well as the contribution she made to Derbyshire throughout her time at Chatsworth, will not easily be forgotten and we shall miss her so very much."
The Dowager Duchess, known to her friends as Debo, was the last of the Mitford sisters, who both fascinated, and occasionally scandalised, British society in the 1940s.
The most notorious of the siblings were Unity, who was a friend of Hitler, and Diana, the second wife of British fascist leader Sir Oswald Mosley. Jessica was a left-wing activist, and Nancy, a novelist.
Deborah moved to Chatsworth in the Peak District after marrying Andrew Cavendish, who became the 11th Duke of Devonshire, and proved to have a shrewd business mind; she transformed the house from ruin into a leading tourist attraction – last year Chatsworth attracted more than 600,000 visitors.