Juan José Eguiara y Eguren published his Biblioteca Mexicana in response to the text of Martí, which denigrated the attainments of the men of letters of the New World in his "epistolas latinas" printed in Madrid in 1735.

In 1686 he moved to Rome where he published the Latin poem Sylva de Tiberis alluvione (1688) and devoted himself to the study of Classical Greek.

He entered the service of Cardinal José Saenz d'Aguirre and wrote a series of Latin poems that remained unpublished.

In 1694 he published the Satyromastix, a vicious attack against Monsignor Lodovico Sergardi who, under the pseudonym of Q. Sectano, had written a collection of Latin Satires against Giovanni Vincenzo Gravina.

In 1715 he returned to Madrid, where Guillaume Daubenton, the French confessor of king Philip V, rejected his candidacy for royal librarian.