Yes they did, however this was not the only currency. Cacao beans were used for small-scale purchases, but large scale purchases were typically made with quachtli, or large bolts of cloth of standardized quality. Additionally, other cultures used other kinds of currency. A common currency good in southern and western Mexico were known as "axe-monies." These were copper or copper-alloy axe heads. These were also used for trade in the area around the Isthmus of Tehuantepec and the Western Yucatan at the time of contact. In fact, the first Spanish to arrive in the region assumed the axes were made of gold and purchased a large number of them before they figured out they were copper. They weren't necessarily designed to be used as axes, but were often used to pay tribute or as currency for market exchange.

It seems like a perishable foodstuff couldn't have been the backbone for an entire economy, but the only info I can find on google is from non-reputable sources.

Why not? It's actually fairly common for ancient states. Many transactions in ancient Egypt, such as payments to workers, were made in grain. One medium of exchange isn't somehow less arbitrary than another. Gold and silver are more permanent materials, but really a commodity money can be made from anything that is widely recognized as having a fixed value.

Additionally, how did they stop counterfeit or inflation? Wouldn't it be possible for someone to simply have a grove of Cocoa trees (Or whatever it is that spawns the beans) out in the country?

/u/snickeringshadow Is probably the most knowledgeable on this subject.