The Outlander cast and crew spent several months filming in South Africa. Many locations for season 3 were provided by Cape Town Film Studios, which will be well known to those who watched Black Sails. Much of the Black Sails set was used, allowing filmilng of many ship-based sequences as well as providing sets for the Caribbean scenes.
The other location used in South Africa was the Theology Faculty Building at the University of Stellenbosch. Those who have read Voyager (Outlander book 3), should have a fair idea of for what that building was used.