The royal couple will attend a ceremony at the town hall and later visit a British warship, the HMS Iron Duke, docked in the city.
They will be accompanied by French defence minister Sebastien Lecornu.
Afterwards, Charles and Camilla will attend a ceremony in the square in front of the old stock exchange.
His Majesty, a keen environmentalist, will also visit a sustainable vineyard in Bordeaux with the Queen.
The city is famous for its wine; it is also home to around 39,000 Britons and is twinned with Bristol.
As he became the first British monarch to address the French senate on Thursday, the King spoke of the “shared link” between the two cities as one of a “countless number of connections” between the UK and France.