Zombie Calavera: Prologue is a game about Santos Gimenez, the former Mexican graveyard guard. Six years earlier, his wife María Fernanda was kidnapped by Pellejo Martinez and his minions. Martinez used a dark ritual to bring back an old Aztec priest's guard from the dead, burning the village of Ataualtepec in the process. Gimenez has been training for six years and is now ready to get his revenge and bring back his wife from purgatory, where she was taken by Martinez. However, his rage has consumed him, turning him into a creature without flesh with red lights in his skull. This 2D platform game consists of a large level composed of several single-screen rooms connected horizontally and vertically using the flip-screen mechanic, offering an amount of freedom to explore. The player must complete many platforming sections to progress. To open the gate to purgatory, Gimenez needs to collect sixteen crucifixes. Once all have been found, the game ends.
The game has a distinct visual style where almost anything is black except for the background and a few elements highlighted in bright colour. Unusually, the player can shoot enemies using a shotgun with unlimited bullets, instead of just avoiding them. The game keeps track of the number of enemies killed.
Dead enemies do not disappear but reincarnate immediately as winged creatures that cannot be killed. Avoiding them is still a possible tactic and even encouraged. The blackness can be used to an advantage, allowing Gimenez to blend into the background, making enemies lose track of him. They then eventually disappear from the screen, but can return in a later level. This makes the game a tactical, slower-paced game where stealth is an important element. Gimenez starts with 66 health, and every enemy encounter drains his meter a little.