He was probably born in the town of Trujillo, in present-day Extremadura, Spain, in the first years of the 16th century and travelled to the Spanish colonies in the Americas as a young man.

The expedition was to be resupplied with stores and provisions delivered by ships traveling north up the Sea of Cortés (Gulf of California), the commander of which would be Alarcón.

The meeting with Coronado was never effected, though Alarcón reached the appointed place and left letters, which were soon afterward discovered by Melchor Díaz, another explorer.

Alarcón eventually sailed to the northern terminus of the Gulf of California and completed the explorations begun by Francisco de Ulloa the preceding year.

Alarcón is unusual among 16th-century conquistadores for his reportedly humane treatment of the Indians he met, as opposed to the often reckless and cruel behavior known from accounts of his contemporaries.