When he returned, he lived as a hermit for several years, wandering and preaching before joining the Cistercian abbey of Sambucina near Luzzi in Calabria, as a lay brother without taking the religious habit.

In 1182 Joachim appealed to Pope Lucius III, who relieved him of the temporal care of his abbey, and warmly approved of his work, bidding him to continue it in whatever monastery he thought best.

There the young monk, Lucas (afterwards Archbishop of Cosenza), who acted as his secretary, was amazed to see so famous and eloquent a man wearing such rags, and the wonderful devotion with which he preached and said Mass.

He refused the request of King Tancred of Sicily (r. 1189–1194) to move his new religious foundation to the existing Cistercian monastery of Santa Maria della Matina.

On Good Friday in 1196, Empress Constance, also Queen of Sicily, summoned Joachim of Fiore to Palermo to hear her confession in the Palatine Chapel.

In this period, instead of the parousia (second Advent of Christ), a new epoch of peace and concord would begin; also, a new religious "order" of spiritual men would arise, thus making the present hierarchy of the Church almost unnecessary.

Among the Spirituals, the stricter branch of the Franciscans, a Joachite group arose, many of whom saw Antichrist already in the world in the person of Frederick II, Holy Roman Emperor (who died in 1250).

As the appointed year approached, spurious works began to circulate under Joachim's name: De Oneribus Prophetarum, an Expositio Sybillae et Merlini ("Exposition of the Sibyl and Merlin") and commentaries on the prophecies of Jeremiah and Isaiah.

In 1263, the archbishop Fiorenzo enhanced the condemnation of his writings and those of his follower Gerardo of Borgo San Donnino, joining a commission in the Synod of Arles, in which Joachim's theories were declared heretical.

It has been argued that the Divine Comedy of Dante Alighieri is largely inspired by the ideas of the Abbot using the interpretation given by his follower Pietro di Giovanni Olivi, active in Florence at the end of the XIII century.

"[18] (Rendered in contemporary English: "Joachim the Prophet, who by numbers formal, natural, and rational, foreseeing, concluding, and foretelling, great particular events, long before their coming.")

Joris-Karls Huysmans' novella Là-bas makes reference to Joachim de Fiore's millenarian eschatology in its concluding scenes, with several characters espousing similar views; presaging the protagonist's conversion to Catholicism.

W. B. Yeats's short story "The Tables of the Law" tells about a single surviving copy of a certain book by Joachim of Flora and its powerful effects on its owner.