Fernando Martins was born in Lisbon, Portugal. While fifteenth century writers state that his parents were Vicente Martins and Teresa Pais Taveira, and that his father was the brother of Pedro Martins de Bulhões, the ancestor of the Bulhão or Bulhões family, Niccolò Dal-Gal views this as less certain. His wealthy and noble family arranged for him to be instructed at the local cathedral school. At the age of fifteen, he entered the community of Canons Regular at the Augustinian Abbey of Saint Vincent on the outskirts of Lisbon.
In 1212, distracted by frequent visits from family and friends, he asked to be transferred to the motherhouse of the congregation, the Abbey of Santa Cruz in Coimbra, then the capital of Portugal. There the young Fernando studied theology and Latin.
After his ordination to the priesthood, Fernando was named guestmaster and placed in charge of hospitality for the abbey. While he was in Coimbra, some Franciscan friars arrived and settled at a small hermitage outside Coimbra dedicated to Saint Anthony of Egypt. Fernando was strongly attracted to the simple, evangelical lifestyle of the friars, whose order had been founded only eleven years prior. News arrived that five Franciscans had been beheaded in Morocco, the first of their order to be killed. King Afonso ransomed their bodies to be returned and buried as martyrs in the Abbey of Santa Cruz. Inspired by their example, Fernando obtained permission from church authorities to leave the Canons Regular to join the new Franciscan Order. Upon his admission to the life of the friars, he joined the small hermitage in Olivais, adopting the name Anthony (from the name of the chapel located there, dedicated to Saint Anthony the Great), by which he was to be known.
Anthony then set out for Morocco, in fulfillment of his new vocation. However, he fell seriously ill in Morocco and set sail back for Portugal in hope of regaining his health. On the return voyage the ship was blown off course and landed in Sicily.
From Sicily he made his way to Tuscany where he was assigned to a convent of the order, but he met with difficulty on account of his sickly appearance. He was finally assigned to the rural hermitage of San Paolo near Forlì, Romagna, a choice made after considering his poor health. There he had recourse to a cell one of the friars had made in a nearby cave, spending time in private prayer and study.