Tomatoes were being cultivated in Mesoamerica by around 500 BC. I'd have thought that they would have been used for something like a soup at least occasionally, long before the Spanish arrived.
https://en.wikipedia.org/wiki/Tomato#Mesoamerica
Likewise, the chilli pepper is from the Americas - and using them to spice up some otherwise iffy meat may well go back to the dawn of the cooking pot. The BBC says that they were being used in cooking 6000 years ago.
http://news.bbc.co.uk/1/hi/world/americas/6367299.stm