Rishi Sunak was driven to Crathie Kirk separately from Charles and Camilla before they attended the traditional Sunday service together.
The King, wearing a kilt, sat next to the Queen, who wore a green coat and hat and clutched a beige handbag on her lap, as they were driven to the 19th century parish church, which overlooks the River Dee.
They were also joined at the church by Charles’s sister the Princess Royal and her husband Vice Admiral Sir Tim Laurence.
The royals are days away from the first anniversary of Queen Elizabeth II’s death and the King’s accession on September 8.
Mr Sunak’s stay at Balmoral Castle – an annual September tradition for sitting prime ministers – comes as he prepares for Parliament to return on Monday after the summer recess.
Charles followed his late mother’s custom by inviting the Prime Minister to join him at his Aberdeenshire retreat, where the royal family spend time each summer.
Former prime minister David Cameron once said there was not much “chillaxing” – chilling out and relaxing – at the castle, with the royals spending their time on outdoor pursuits.
Years of memories have been forged at Balmoral, including of family barbecues – where Prince Philip, the late duke of Edinburgh, did the cooking and the late queen did the washing-up.
At royal residences, servants meticulously unpack luggage for guests.
Cherie Blair said in her autobiography her son Leo was conceived at Balmoral after she left her contraception at home out of embarrassment before her annual weekend stay there with husband and then-prime minister Sir Tony Blair.
“In 1998 – I had been extremely disconcerted to discover that everything of mine had been unpacked,” she wrote.
“Not only my clothes, but the entire contents of my distinctly ancient toilet bag with its range of unmentionables.
“This year I had been a little more circumspect, and had not packed my contraceptive equipment out of sheer embarrassment.
“As usual up there, it had been bitterly cold, and what with one thing and another…”