The king was joined by Queen Consort Camilla for Friday’s service at Crathie Kirk, which commemorated the life and service of Britain’s longest-serving monarch.
Queen Elizabeth was 96 when died at her beloved Balmoral home on September 8 last year in her platinum jubilee year, after reigning for seven decades.
The king and his wife went on a walkabout after the service, which was also attended by other family members, including the late queen's niece and nephew, Lady Sarah Chatto and the Earl of Snowdon, who were close to their aunt.
The king and queen smiled and shared jokes with Balmoral estate staff, members of the royal household and residents from the nearby town of Ballater, who treated the late monarch as one their own.
The Rev Kenneth Mackenzie, minister of Crathie Kirk, who officiated at the event, said: "It was a simple reflective time, a time when we were able to give thanks for the life of the late queen and recognise the poignancy of this day for that family and this community, as well as the nation and Commonwealth.
"I think that those of us who did get to see the queen in different situations, but particularly up here, felt it today, were reminded of the loss.
"But we were also glad, just as the family were able to gather here last year, some members of the family were able to be here.
"And wherever they might be, in their own homes or wherever, I'm glad that people will have the opportunity to reflect and give some thanks for the life of the queen."
The event was a deeply personal moment for the king, who recorded a message and released a favourite photograph of his mother to mark the anniversary of her death.
In words written and recorded at Balmoral Castle, he said he recalled with "great affection her long life, devoted service and all she meant to so many of us".
He added: "I am deeply grateful, too, for the love and support that has been shown to my wife and myself during this year as we do our utmost to be of service to you all."
UK marks first anniversary of death of Queen Elizabeth II - in pictures
The formal colour photograph chosen by King Charles was taken by Cecil Beaton and shows the Queen in 1968.
The Prince and Princess of Wales visited the Welsh cathedral of St Davids for a short private service on Friday.
The service, with prayers in English and Welsh, reflected on nd celebrated the life of the queen.
An incredibly poignant moment of the service was the singing of Thou knowest, Lord, the secrets of our hearts.
It evoked the sadness and emotion of the funeral 12 month ago.
The most moving moment of the service though was when Prince William accompanied his wife, Kate, to place flowers next to an image of the late queen.
The couple stood before the image in the totally silent cathedral to reflect on the life of the late monarch.
They had earlier paid their own online tribute to the late queen on the anniversary of her death, saying: "We all miss you."
The message, written by Prince William and Kate on Twitter, now known as X, said: "Today we remember the extraordinary life and legacy of Her Late Majesty Queen Elizabeth. We all miss you. W & C."
It was accompanied by a family photograph of the late monarch surrounded by her great-grandchildren, including Prince George, Princess Charlotte and Prince Louis, and her two youngest grandchildren.
Prince William's brother, Harry, the Duke of Sussex, visited St George’s Chapel, Windsor, on the first anniversary of the late Queen’s death.
The King George VI Memorial Chapel, which sits within the walls of St George’s Chapel, is the late queen's final resting place. An image of Harry leaving St George’s on Friday morning circulated on social media.
Other members of the family also paid tribute.
Princess Eugenie remembered her grandmother, writing on Instagram: "Thinking of you today. Missing you so much."
She included a personal memory – an image of herself sitting next to her grandmother in the sunshine on a wooden bench outside what appeared to be a cabin on the Balmoral estate.
The late queen's senior dresser and confidante, Angela Kelly, also posted a moving message addressed to Elizabeth II, saying: "I will never forget you. I will always love you. I miss you my friend."
Ms Kelly, who worked for the queen for more than 25 years and had an unparalleled bond with the monarch, was staying at Balmoral the week she died.
Soldiers and horses who took part in the state funeral procession and proclamation salutes signifying the new reign returned to perform Accession Day gun anniversary salutes in the king's honour on Friday.
Capt Amy Cooper, who was the lead rider in the procession that carried the queen's coffin to lie in state in Westminster Hall, gave the order to fire a 41-gun salute at midday in London's Hyde Park.
Almost all of the King's Troop riding out – in their distinctive dress uniform of gold braided jackets and busby hats accompanied by the Band of the Grenadier Guards – played a role in the final farewell to the queen a year ago.
A 62-gun salute was also fired at the Tower of London by The Honourable Artillery Company – with the regiment and the King's Troop both responsible for gun salutes after the death of Queen Elizabeth.
Bells also rang out at Westminster Abbey at 1pm in commemoration of the King Charles's accession.