The official Palace beekeeper, John Chapple, said he travelled to Buckingham Palace and Clarence House on Friday, following news of the Queen’s death, to carry out the ritual.
He told the bees that their new master is now King Charles III and placed black bow ribbons onto the hives.
Speaking to MailOnline, he said: “I’m at the hives now and it is traditional when someone dies that you go to the hives and say a little prayer and put a black ribbon on the hive.
“I drape the hives with black ribbon with a bow.
“The person who has died is the master or mistress of the hives, someone important in the family who dies and you don’t get any more important than the Queen, do you?
“You knock on each hive and say, ‘The mistress is dead, but don’t you go. Your master will be a good master to you.’”
The ritual is carried out because custom has it that not to tell bees of a change of owner would lead to the bees not producing honey, leaving the hive or even dying.
The 79-year-old takes care of over a million bees at the height of summer, as there are two hives in Clarence House and five hives in Buckingham Palace.
However, at this time of year, their numbers drop, meaning each hive contains around 20,000 bees.
The bee-keeper, who has worked at the palace for fifteen years, told the publication he hoped to continue looking after the bees under the new King.
“It has been a wonderful privilege to do things like this for the Queen and hopefully now for the King,” he said.
“I hope they still want to keep the bees on their premises. You never know. They might say, take them away but I don’t think that will happening though really you do never know.
“It’s up to the new tenant of Buckingham Palace.”