In the Municipal Palace at Plaza Regocijo, this museum has exhibitions of contemporary art. Admission with the boleto turistico
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A shop ("museum") explaining the history of cacao (free) and offering chocolate workshops (not free) as well as cacao farm tours (not free). Different recipes from around the world are available all made with chocolate from the factory inside the cacao and chocolate museum. Great artisanal and organically sourced hot chocolate.
In the home of the Inca historian Garcilaso de la Vega, this 2-story museum has many paintings from the 17th and 18th century as well as historical displays chronicling the pre-Hispanic Inca civilization, the invasion of the Spanish and the role of Christianity in the post-conquest era. A tour is unlikely to take much more than an hour.
The park square has churches, shops, restaurants and bars surrounding it, and is a great place to spend an afternoon. The historical center of Cuzco is beautiful, but you will have to deal with all the street vendors and hawkers of cheap paintings and other souvenirs. They are everywhere in and around the Plaza de Armas. They somewhat spoil the experience.
A great place to visit one of Cuzco's many great coffee shops. Next to the Plaza is the main market, which is fairly traditional and is a worthwhile visit. The market has a mix of stalls selling food and other household items as well as clothing and souvenirs.
Catedral Basílica de la Virgen de la Asunción
Elaborate large cathedral full of colonial-era religious paintings. The biggest church in Cuzco, in front of Plaza de Armas. As a tourist the entrance is S/25. If you go in a "misa" (mass) between 06:30–09:00, it is free. No photography allowed.
Extensive museum of pre-Inca, Inca, and colonial artifacts. Labels in English and Spanish, though the descriptions in English are sometimes pretty different from the ones in Spanish.