[1] At one time Pérez held the office of contador (accountant) to the Queen of Spain, showing he was of noble family.

Father Francisco Gonzaga, Minister General of the Observant branch of the Order (1579–87), declared that La Rábida belonged to the Franciscan Custody of Seville, which, by decree of Pope Alexander VI on 21 September 1500, was raised to the rank of a province.

The historian Francisco López de Gómara in 1552 seems to have started the blunder, copied by almost every subsequent writer on the subject, of making the two names Perez and Marchena serve to describe one and the same person by speaking of the Father Guardian of La Rábida as Friar Juan Perez de Marchena.

[3] It was Pérez who persuaded the navigator not to leave Spain without consulting Isabella, when, footsore and dispirited, he arrived at La Rábida, determined to submit his plan to the King of France.

Whether he returned to La Rábida or died in America is uncertain; in the legal dispute between Diego and Columbus, the royal fiscal (attorney general), Dr. García Hernándes, testified in 1513 that Pérez was then dead.