Mendoza, a Spanish navigator trained by Ferdinand Magellan, is renowned for successfully piloting ships past the perilous Cape Horn coast three times. His past includes Magellan's circumnavigation expedition, where he rescued the infant Esteban from a sinking ship west of the Strait of Magellan. A powerful wave separated him from the boy's father, allowing only Esteban's rescue. During this event, Mendoza took one half of Esteban's sun medallion, convinced their fates were linked. This medallion fragment later became the focus of his ten-year research into the Mysterious Cities of Gold.

Initially driven by an intense desire for riches, Mendoza positions himself as the unofficial leader in the quest for the Cities of Gold. He displays cunning and self-serving tendencies, manipulating circumstances to his advantage. He exploits the orphaned Esteban's grief and curiosity, persuading the boy to join his voyage to the New World by suggesting his father might still be alive and presenting the medallion piece as proof of their connection. He also orchestrated Zia's kidnapping to utilize her ability to read Inca quipus, concealing her aboard the ship *Esperanza* without Esteban's knowledge.

Mendoza exhibits complex duality throughout his journey. While often pragmatic and harsh—particularly towards his associates Sancho and Pedro, whom he chastises and treats dismissively—his interactions with Esteban, Zia, and Tao reveal deeper facets. His initial self-interest shifts as he repeatedly prioritizes the children's safety over his pursuit of gold, protecting them from capture and ensuring their quest continues. This protective instinct strengthens during conflicts with antagonists like the Olmecs and Spanish soldiers. By the climax of the first story arc, he actively aids the children against the Olmecs, motivated by genuine concern rather than personal gain.

His relationships illustrate this development. With Esteban, Mendoza evolves from a manipulative figure into a reluctant guardian, eventually acknowledging his role in Esteban's past by confirming the High Priest of the City of Gold was Esteban's father. He transitions from viewing Zia and Tao as tools to valuing them as wards, offering them guidance and protection. His dynamic with Sancho and Pedro remains largely transactional, though their loyalty persists despite his harshness. In later seasons, Mendoza encounters Isabella Laguerra, a sword-wielding ally of the antagonist Zarès. Their initial rivalry evolves into mutual respect and eventually a romantic connection.

Following the destruction of the first City of Gold, Mendoza returns to Spain with salvaged gold alongside Sancho and Pedro, intending to rejoin the children later. His eventual reunion with them underscores his enduring commitment to their well-being, even as his ambitions for wealth diminish.