Little is known about Alarcón's life outside of his expedition in New Spain. He set sail on May 9, 1540 with orders from the Spanish Viceroy Antonio de Mendoza to await at a certain point on the coast the arrival of an expedition by land under the command of Coronado.
He sailed into the Gulf of California, which had been explored the previous summer by Francisco de Ulloa. He made a careful survey of the coast, and on 26 September ascended the Colorado River (then called the Río del Tizón or Río de Buena Guía) for 85 Spanish miles, being the first European to do so. The meeting with Coronado was not effected, however, although Alarcón reached the appointed place and left letters, which were soon afterwards found by Melchior Diaz, another explorer.
Ulloa and Alarcón were the first to determine that Baja California was a peninsula and not an island, as had been supposed at the time of its initial discovery. Upon Alarcón's return to New Spain in 1541 he prepared a more accurate map of California depicting it correctly as a peninsula. Subsequent sixteenth century maps accepted these findings, the notion of the Island of California arose again in the seventeenth century and persisted on many European maps well into the eighteenth century.