The Incas built the temple known as Kiswarkancha on the main square in Cusco. It was the Inca palace of Viracocha, ruler of the Kingdom of Cusco around a century before the Spanish colonists arrived. The aboriginal name of this city was Qusqu. Although it was used in Quechua, its origin has been found in the Aymara language. The word itself originated in the phrase qusqu wanka ("Rock of the owl"), attending to the foundational myth of the Ayar siblings. Near to the Kiswarkancha was the Suntur Wasi, an armoury and heraldry centre for the Inca royalty. When the Spanish conquistadores arrived in Cuzco, they decided to take down the temple and build their Christian cathedral in that prominent site. The cathedral's construction began in 1559 on the foundations of Kiswarkancha. It is shaped like a Latin cross. The location of Viracocha's palace was chosen for the purpose of removing the Inca religion from Cusco, and replacing it with Spanish Catholic Christianity. Because 1559 was only 26 years after the conquistadores entered Cusco in 1533, the vast majority of the population was still of Quechua Inca descent. The Spaniards used the Incas as a labour workforce to build the cathedral. The original designs for the 1-acre (4,000 m2) large construction were drawn by the Spanish architect and conquistador, Juan Miguel de Veramendi. His design of a Latin cross shape incorporated a three-aisled nave, where the roof was supported by only 14 pillars. Over the 95 years of its construction, the building work was supervised by Spanish priests and architects, until its completion in 1654. Most of the stones from the building were taken from Sacsayhuamán, an Inca holy and defensive structure located on the hills above Cusco. Due to its large size, much of Sacsayhuamán remains intact. Just as the temple of Viracocha was removed and the holy stones of Sacsayhuamán were employed to build the cathedral, the intentional desecration of Inca religious architecture, once the Spaniards learned that the very sand spread on Cusco's main plaza was considered sacred, they removed it and employed it in the cathedral's mortar. The Gothic-Renaissance style of the cathedral reflects that of Spain during the period of the Spanish conquest of South America and also Cusco. There is also evidence of Baroque influence in the facade on the Plaza de Armas. The Incas incorporated some of their religious symbolism into the cathedral, for example, the carved head of a jaguar (an important god or religious motif found widely through much of ancient Peru) is part of the cathedral doors.

Originally named Intikancha or Intiwasi, it was dedicated to Inti, and is located at the old Inca capital of Cusco. Mostly destroyed after the 16th century war with the Spanish conquistadors, much of its stonework forms the foundation of the Santo Domingo church and convent. To construct Coricancha, the Inca utilized ashlar masonry, which is composed of similarly sized cuboid stones. The use of ashlar masonry made the temple much more difficult to construct, as the Inca did not use any stone with a slight imperfection or break. By choosing this masonry type, the Inca intentionally demonstrated the importance of the building through the extent of the labor necessary to build the structure. Through the arduous labor needed to construct buildings with ashlar masonry, this form of construction came to signify the Inca's imperial power to mobilize local labor forces. The replication throughout Andean South America of Inca architectural techniques such as those employed at Coricancha further illustrates the Inca's control over a vast geographic region. Pachacuti Inca Yupanqui rebuilt Cusco and the House of the Sun, enriching it with more oracles and edifices, and adding plates of fine gold. He provided vases of gold and silver for the Mama-cunas, nuns, to use in the veneration services. Finally, he took the bodies of the seven deceased Incas and enriched them with masks, head-dresses, medals, bracelets, sceptres of gold, placing them on a golden bench. The walls were once covered in sheets of gold, and its adjacent courtyard was filled with golden statues. Spanish reports tell of its opulence that was "fabulous beyond belief". When the Spanish required the Inca to raise a ransom in gold for the life of the leader Atahualpa, most of the gold was collected from Coricancha. The Spanish colonists built the Church of Santo Domingo on the site, demolishing the temple and using its foundations for the cathedral. Construction took most of a century. This is one of numerous sites where the Spanish incorporated Inca stonework into the structure of a colonial building. Major earthquakes severely damaged the church, but the Inca stone walls, built out of huge, tightly interlocking blocks of stone, still stand due to their sophisticated stone masonry. Nearby is an underground archaeological museum that contains mummies, textiles, and sacred idols from the site.

The term Sacsayhuaman means in Quechua “place where the hawk is satiated”. The name is surely due to the presence of these birds. It is presumed that it was a fortress, although it is also believed that it could be a ceremonial center. Due to its structure with a military aspect, the Spaniards, on their arrival in the 16th century, would have named it a ‘fortress’. When the Spanish attack was repulsed there during the Inca rebellion in Vilcabamba, the place served as an Inca fortress. The architecture in Sacsayhuaman has sacred buildings such as residential buildings, towers, shrines, warehouses, roads and aqueducts. That is why, the shape and harmony of the landscape is similar to other sacred Inca places such as Machu Picchu. The main wall of Sacsayhuaman is built in zigzag with giant stones up to 5 meters high and 2.5 meters wide (between 90 and 125 tons of weight). The south side is bounded by a polished wall approximately 400 meters long. The east and west are limited by other walls and platforms. According to the Peruvian chronicler Inca Garcilaso de la Vega, Sacsayhuaman was the greatest architectural work that the Incas built during its apogee. Sacsayhuaman offers an amazing view of Cusco. You can see the summits of Ausangate, Pachatusán and Cinca. These summits were considered sacred to the Incas. The archaeological complex itself has very amazing places, some of them with history and meaning.

The Incan Empire was completely destroyed by European forces in the 16th century. Many of their massive temples, fortresses and cities were left standing, but without any clues as to their purpose. Qenqo Temple, fifteen minutes from Cusco is similarly mysterious and a dark account has formed in the historical vacuum. In Quechua, Qenqo means labyrinth or zig-zag and the temple is named for the crooked canal cut out of its rock. Although it is clear the canal carried some sort of liquid, researchers have been forced to guess at its purpose, and at what liquid it transported. Hypotheses range from carrying holy water, chicha (corn beer), or blood. All three indicate that Qenqo was used for death rituals, possibly to embalm bodies or detect whether a person lived a good life by the course the liquid followed. Qenqo is a unique temple in its construction as well, having been entirely carved out of a gigantic monolith. Stretched across a hillside, the temple is carved out of rock and marries the man-made tunnels with natural chambers. One of these chambers features 19 small niches and is set up as an amphitheater. Once again, the purpose of the theater has been lost over time, but most agree the area was used for some type of sacrifice to the sun, moon and star gods who were worshipped at the site.

Puca Pucara houses enclosures such as inner squares, canals, aqueducts, baths and a well-known ancient road, which should have been part of the network of Inca roads known as Qhapaq Ñan; The buildings are built with rocks of different sizes (small and medium). Puca Pucara presents the surface of the rocks very uneven, compared to other archaeological sites. The name Puca Pucara means red fort , and is due to the location of the archaeological group and to the existence of some semi-circular enclosure; Red is the color of the earth. The name of this place was used from the twentieth century. The constructors of the Inca Civilization built three walls of irregular plant, that establish the three levels of the site. The first wall presents a sinuous path, which carefully avoids cutting the protruding rocks. From the north end at the back of the outer wall, you can find a total of 6 rooms of different sizes; Arranged irregularly in order to avoid touching the stones that make up the wall. To the west you will find a high place of trapezoidal form that can be entered from an outside staircase. In ancient times the square was surrounded by buildings on two sides. The 9 rooms regularly laid out in this place do not appear to have been in any way fortified enclosures. The second wall is located around the central elevation. These first two walls, have wide platforms to the east and south of the site. At the back of the second wall, it is possible to find 3 different rooms of the typical Inca architecture, since 2 of them do not have the common rectangular but trapezoidal floor. The third wall is surrounding the summit and there is no trace of the buildings that could exist in this place. The buildings were built with stones of many sizes between medium and small, the surface of the rocks is very uneven compared to other archaeological remains of the Inca civilization. The urban layout presents an adequate and functional layout. According to some chroniclers, in pre-Hispanic times, when the Inca prepared to visit the baths located in Tambomachay, his entourage composed of soldiers and dancers, they remained in Puca Pucara , which simultaneously operated as barracks and tambo(hostel). Rumors exist about a chincana (tunnel), supposed to function as a channel of communication between these 2 Inca towns.

Tambomachay is an Inca archaeological site located just outside Cusco. Its precise function is unknown, but it may have served as a ceremonial site, an Inca spa, or a military outpost—or perhaps a mix of all three. Tambomachay sits on a hill about 4 miles north of Cusco, at about 12,150 feet (3,700 meters) above sea level. The structure consists of three stepped terraces of precise Inca stonework, with trapezoidal niches built into some of the retaining walls. The whole thing is built over, or into, a natural spring, which continuously feeds a series of small aqueducts, canals, and waterfalls built into the terraces. The site is also known as El Baño del Inca, or the Bath of the Inca. This refers to one of the long-held theories about the site’s function: that it was a spa of sorts for the Inca ruler, and maybe for the wider Inca nobility. It’s a secluded and tranquil spot, and the constantly flowing water would certainly have provided for all the Inca’s spa-break needs. But there was probably more going on at Tambomachay than just high-altitude bathing.