Jewels of Cleopatra 2: Aztec Mysteries is, at its core, your standard match-three puzzle casual game. You are presented with a board, and by switching adjacent tiles, you line up three or more pieces to make them disappear. Similar to
Jewel Quest, the squares that have been activated are turned gold. Unlike most games of this style, instead of trying to turn all of the squares gold or just collect a certain number of points, you are trying to lay out a path of gold squares for Turnstone to walk through in order to make it to the next level of the temple.
The levels start off fairly small, with only a few screens worth of tiles, but it isn't long before the areas become large and full of traps, critters or switches. Also, scattered throughout each level are larger squares that will send you into one of 12 mini-games. While most of the time you can pass them by if you are running low on time, there are a few that lie in your path to the level's exit. These mini-games are inspired by games like whack-a-mole, slot machines, memory and various other little games that can be picked up pretty easily and typically involve more chance than skill.
There are five temples of levels, and before you leave the temple, you will have three non-standard levels. One is an armadillo race where you point your assistant's pet treasure-hunting armadillo around a small track alongside other armadillos. It's an odd thing to insert into a game like this, but it does break up the potentially repetitive nature of the game. Once you are past the race, you will have to take a carving that Turnstone finds and re-arrange it so it looks correct. Finally, the last level of the temple is just like the normal ones, except your rival McGrady is also trying to get to the exit, except he doesn't have to walk on gold-colored tiles, so the normal race against time is a bit quicker paced.