His Majesty and Prime Cabinet Secretary Musalia Mudavadi boarded an Admiral Barge from the Mombasa ferry site that sailed to the naval base as locals watched the historic moment from a distance.
At the base, they were welcomed by President William Ruto, his deputy Rigathi Gachagua, and other dignitaries.
King Charles and President Ruto did not make speeches during the tour but could be seen exchanging pleasantries as the soldiers landed on the shores of the Indian Ocean.
Also present were Defence Cabinet Secretary Aden Duale, the Chief of Defence Forces, and the Commanders of the Kenya Army, Navy and Air Force.
The King inspected a guard of honour before a march past took place.
The King and Queen proceeded to the beachhead, where their Majesties witnessed the Kenya Marines demonstrate a covert beach landing.
Accompanied by President Ruto and the Commander of the Kenyan Navy, His Majesty proceeded to the dais for a salute by the guard of honour followed by the British and Kenyan national anthems played by a military band.
Their Majesties then walked to the jetty and bade farewell before departing the Mtongwe Naval Base for Nyali Beach.
Dressed in a grey suit, white shirt, and matching shoes, the King arrived at Nyali Beach within Mombasa Marine Park to witness how community groups and Kenya Wildlife Service (KWS) have been managing waste, including plastics and conserving endangered turtles.
He was welcomed by the senior principal research scientist at Kenya Wildlife Service Mohamed Omar and Early Birds Banda Nyali beach patron Abeid Mahmoud, Scouts and Girl Guides.
The King spent time listening to the various groups and viewing handicraft items displayed at the beach made from recycled waste.
He wound up at the enclosed turtle hatchery, where Dr Omar and Mr Mahmoud explained that it was established early this year to save endangered turtles.
"This beach is a nesting area for turtles, but they are endangered by predators, including upcoming construction. Early Birds Banda youth collect turtles with the support of KWS and keep them in the hatchery, where most of them hatch," said Mahmoud, who is also a KWS honourary warden.
Mahmoud said since January this year, they have collected 1,307 turtle eggs and successfully hatched 1,112.
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Mahmoud explained that British High Commissioner to Kenya Neil Wigan visited Nyali Beach a month ago and was impressed by the community groups' conservation efforts.
The King is today expected to visit Mombasa ACK Memorial Cathedral, Fort Jesus and Mandhry Mosque on Mombasa island.