By the time the conquistadors arrived the locals already had suffered destruction and massive population loss....
It was very little to deal with guns and germs......
A TV programme about the Inca empire showed how the network was organised around food production and distribution, with large, still extant, store-houses at strategic points. The technique of terracing basins protected by mountains seems to have created a series of micro-climates, enabling a variety of crops to be grown at different levels.
The programme also showed the mummified body of a young Inca woman who'd died not long after the Conquistadors' arrival. She hadn't died from disease, European or home-grown, but from malnutrition. The Incan population was presumably as susceptible to diseases as any other but the main culprit seems to have been malnutrition which, if it doesn't kill you immediately, certainly lowers resistance.