I did some quick research. Though Pizarro and his band took Cuzco and decapitated the Inca leadership ridiculously quickly, there was a number of rebellions afterwards and so the Spanish conquest of Peru is usually regarded as having taken until 1572, when the Tupac Amaru rebellion was crushed, to complete.
The contrast is with Mexico, where while the Aztecs get the attention, they hadn't taken all of Meso-America and there were other native american states. And here we see the Spanish fighting in a major war in 1560-90, and the last Mayans were defeated and brought under Spanish rule sometime in the seventeenth century.
This is one of those things that would have made a big difference in the century the POD had occurred, with butterflies due to people dying at different times and marrying different spouses than OTL. The Spanish conquest of Peru follows the Mexican pattern, with them quickly seizing the main native state, which is historically regarded as THE conquest, but then gradually fighting and conquering the other states, instead of taking everything over at once and then fighting off a series of rebellions (including by some of the conquistadors). But the end result is the same.