They were driven through the streets of the capital to Llandaff Cathedral, having landed nearby in a helicopter.
As the new King set foot on Welsh soil, a gun salute was fired by reservists from 104 Regiment Royal Artillery at Cardiff Castle several miles away.
Charles and Camilla were met at the landing site by the Lord Lieutenant of South Glamorgan, Morfudd Meredith.
When they arrived at the cathedral by car, they were greeted Vice Lord Lieutenant Sir Brooke Boothby, whose wife, Lady Boothby, is close friends with Camilla.
The King was wearing a black morning suit and the Queen Consort a black skirt, suit jacket and hat.
Camilla also wore a silver leek brooch, a symbol of Wales, which was a gift from the Queen.
Sir Brooke introduced the royal couple to Wales First Minister Mark Drakeford, High Sheriff of South Glamorgan Rosie Moriarty-Simmonds and Welsh Secretary Robert Buckland, as well as other dignitaries and interfaith leaders.
Camilla commented to Mr Drakeford that they had “brought the sun” with them, adding that it “might be the last day of sunshine for a while”.
The First Minister replied: “We ought to enjoy it then.”
Guided inside the packed cathedral by the Dean of Llandaff, Michael Komor, and Archbishop of Wales Andy John, the King and Queen Consort were led in procession down the aisle by the chaplain to a fanfare before the congregation sang a hymn.
Prime Minister Liz Truss arrived earlier, wearing a long black coat and a black fascinator, and sat in the front row next to Mr Drakeford, Senedd Speaker Elin Jones and Mr Buckland.
A service of prayer and reflection for the life of Queen Elizabeth II then got under way, including the singing of psalms by Llandaff Cathedral Choir and a reading in Welsh and English by Mr Drakeford, taken from the First Book of Kings.
In his address, the Archbishop said the Queen has “graced the life of Wales with love, dignity and courage”.
He added that she was a “monarch who could surprise and delight us”, with the ability to bring people together in difficult circumstances, such as her visit to the site of the 1966 Aberfan disaster, where 144 people lost their lives when a coal tip collapsed on a primary school.
Prayers recorded by a number of faith leaders including John Minkes, from the South Wales Jewish Representative Council, Dr Abdul-Azim Ahmed, from the Muslim Council of Wales, and Bishop of Llandaff June Osborne were then played.
Music was played by Royal Harpist Alis Huws and Catrin Finch, the first ever harpist chosen by the then-Prince of Wales.
Ending the service, the Welsh national anthem, Hen Wlad Fy Nhadau, was sung, followed by a trumpet fanfare and a rendition of God Save The King.
Before leaving, Charles and Camilla signed the cathedral’s visitors’ book.
As she left the cathedral, the Queen Consort was presented with a posy by five-year-old Keira Hillebert, whose parents are from Atlanta, Georgia, in the US.
Keira recently got her British citizenship and received her British passport on the day the Queen died.
Her mother, Krisi, said: “I shook Queen Camilla’s hand and then Keira thought she was supposed to do the same so she grabbed Camilla’s hand and said ‘I’m Keira!’
“She then ran off, saying she was cold.
“They were so lovely and sweet with her and Camilla asked if she had been practising her curtsy because she did it so well.”
The royal couple were then greeted by more than 40 pupils from five primary schools around Cardiff.
Dexter Garland and Ella Noble, both 10, from St Julian’s Primary School in Newport, handed Charles and Camilla a mug each with their own artwork printed on them.
The school opened in the year Queen Elizabeth’s reign began 70 years ago.
Ella said: “The Queen said she appreciated it and would make sure to have a cup of tea in it.
“It is something I will remember for the rest of my life. It was the best experience of my life.”
Charles and Camilla then went on a walk around the Cathedral Green to meet members of the local community and were greeted by loud cheers, and cries of “God Save The King”.
They were handed gifts and flowers, and many people thanked them.
Some people had gathered early in the morning to get a glimpse of the royal visitors, with the first arriving at around 3.30am.
A lone male voice at one point shouted over the crowd: “We pay £100 million a year for you, and for what?”
September 16 is also Owain Glyndwr Day, which celebrates the life and legacy of the “rebel” who is seen as the last native-Welsh Prince of Wales.
Llandaff Cathedral was severely damaged in Glyndwr’s rebellion against English monarch Henry IV, which began in 1400.
The King and Queen Consort will now head to the Senedd, before processing through the city to Cardiff Castle.
A silent anti-monarchy protest is due to be held outside the castle by a number groups who have joined together under the banner Real Democracy Now.
It is the first time Charles has returned to the country as monarch, after serving for 64 years as the Prince of Wales, a title bestowed on him by his mother when he was nine years old.
Wales is the last destination on the tour of nations which the couple embarked on after Charles was proclaimed King, travelling more than 1,500 miles around the UK in his first week on the throne.
The royal visit is being televised for people wishing to stay at home.