The Andes mountains were quite an advantage to the Inca. They gained very important mineral resources like gold and silver and emeralds, as well as copper and tin ( iron being unlikely though). Desert and jungle acted as natural barriers for the empire, as well as peaks and gorges of the mountains that were connected by bridges; and control of these would allow control of their cities. The mountains supplied a good flow of fresh water, and Inca ingenuity created aqueduct systems carved out of the rock itself in order to funnel this water down to cities and towns.
Even 11,000 feet or more in the air, the Inca were able to transform the landscape to use for agriculture, in which terraces on the side of cliffs are evidence of this and can still be seen today. The climate was mainly a dry one and with the help of water coming from the melting glaciers high up on the mountain, the growth of crops excelled, thus the people of the empire were well feed.
The Inca were a highly organized people, and knew how to use geography to their advantage.