Cuzco
The Spanish built their colonial city over the Inca capital, which means in Cusco’s city centre you walk on streets flanked by Spanish baroque buildings sitting on Inca foundations that are demonstrably more durable than what was built on top of them. Earthquakes in 1650 and 1950 destroyed many of the colonial structures; the Inca walls they sat on survived both. Qorikancha, the most important Inca temple, had the Dominican Convent of Santo Domingo constructed around and over it in the 16th century. In the courtyard you can see exactly where the Spanish built and where the Inca stonework runs beneath and beyond it.
The City
Cusco sits at 3,400 metres. The first 24 to 48 hours should be kept physically easy: no trekking, no altitude hikes, limited alcohol. Coca leaf tea (mate de coca) is served as a standard welcome drink at every hotel and is a mild help. Acetazolamide (Diamox) is available at Cusco pharmacies without a prescription and is effective if started a day or two before arrival.
Sacsayhuaman on the hill above the city is a fortified Inca complex built from massive fitted limestone blocks, some weighing over 125 tonnes, assembled without mortar using the earthquake-resistant Inca polygonal technique. The scale is more impressive in person than photographs suggest. A 30 to 40 minute uphill walk from the Plaza de Armas or a short taxi.
Qorikancha: the stripped gold plates are gone (taken by the Spanish in 1533), but the curving Inca stone walls visible in the courtyard beneath the Dominican architecture are some of the finest surviving Inca masonry. Small admission; worth the time.
Plaza de Armas: the cathedral (1559-1654, built on the site of an Inca palace) and the Jesuit church of La Compañia de Jesús flank the square. Guided cathedral tours cover the colonial painting collection and the gold altar.
Sacred Valley and Machu Picchu
The Urubamba Valley northwest has Pisac, Ollantaytambo, and Chinchero. Machu Picchu requires a train (1.5 to 4 hours from different departure points) or a multi-day trek. Train tickets book out weeks to months ahead in peak season (June through August). Entry to Machu Picchu itself is timed and limited; book through the official Peruvian government system in advance.
Where to Eat
Chicha by Gastón Acurio on Plaza Regocijo does elevated Andean cooking in a restored colonial building. Cicciolina on Calle Triunfo is reliable for a broader menu at fair prices. The San Pedro market is the right place for breakfast and lunch at local prices: chicha morada, empanadas, and set lunch menus.