The letter, from 1998, was sent to his interior designer friend Dudley Poplak.
In it, he confided that he was increasingly drawn to the "timeless traditions" of the Orthodox Church, claiming they are the only ones not affected by such issues.
The monarch has had a long-standing connection with the Greek Orthodox Church, influenced by his father, Prince Philip, who was Greek Orthodox before marrying Queen Elizabeth, the head of the Church of England.
In recent years, the Church of England has been accused of being overly focused on political correctness and not standing firm on Christian values, especially regarding its diversity and inclusion efforts and a recent £1bn fund aimed at addressing its historical ties to slavery.
In the same letter, dated August 24, 1998, Charles shared his concerns about Genetically Modified Crops (GMC), referring to them as 'Frankenstein' food. He lamented that "money drives everything" and expressed frustration over a perceived loss of wisdom in the face of powerful companies like Monsanto, which makes genetically engineered crops.
Poplak, who passed away in 2005, was one of several royal-related letters auctioned at Lay's Auctions in Penzance, Cornwall, fetching over £1,700 in total.
Charles's letter about GM crops and the Church sold for £170 earlier this month.
A spokesperson for the auction house told the Daily Mail: "It is an interesting, candid and intriguing letter in which Charles expresses his despair at the prospect of GMO and his interest in the traditions of the Orthodox Church.
"The royal family aren't supposed to make political statements as a rule, certainly in public, but these remarks were made in provate correspondence."