He was already looked upon as a saint in Rome. At the very sight of him quarrels and disputes, unkind or loose talk ceased. But Don Joseph, like all the chosen of God, passed through a time of bitter spiritual trial and desolation. In 1675 he writes to Maria Crocifissa imploring her prayers. She answered exhorting him to patience and humility in accepting his cross from the hand of God, telling him that she, too, was not without her spiritual trials. He answered that the days of actual physical martyrdom are over, and that we are now in the days of hidden martyrdom, seen only by God; the lesson of it all being trust in God. He was at this time so scrupulous that he could not be allowed to hear confessions or preach.

Don Joseph’s life was almost that of a hermit, devoted to prayer and study.
He made a special study of Greek philosophy, Holy Scripture and the Breviary. Knowledge of eastern languages was a necessity, and his Hebrew teacher, Rabbi Moses da Cave, owed his conversion from Judaism in 1698, at the age of seventy and after long years of resistance, to the prayers of Don Giuseppe and his sisters.

   His first book was an edition of the Speculum of St Augustine. In 1680 appeared the Codices Sacramentorum, being four texts of the most ancient liturgies he could meet with. These precious documents had been stolen from the library of Fleury Abbey, and dispersed by the Calvinists in the sixteenth century. They had been gradually collected together again in Rome, partly by Queen Christina of Sweden. Tommasi’s work became celebrated and Mabillon transcribed a great part of it in his Liturgia Gallicana. Out of modesty his next book, the Psalterium, was pub­lished under the name of Giuseppe Caro. It was a work of very great learning, giving an account of the two most important translations of the psalms, the Roman and the Gallican, and it opened up for liturgists a whole new field of research. There were many other treatises of the same class, particularly on the Antiphonarium, all displaying great erudition and fervent piety. His work on the psalms attracted the notice of Pope Innocent XII, and in 1697 Tommasi entered the Vatican, under obedience, for the first time. 

The year 1704 saw him appointed theologian to the Congregation of Discipline of Regulars. In this latter capacity he laboured for the reform of the orders, and all who came in contact with him were impressed with his zeal and holiness.  Don Tommasi, having been chosen as confessor by Cardinal Albani, had required his penitent in 1700 to accept the papacy under pain of mortal sin. Soon after, Clement XI insisted on raising the Theatine scholar to the cardinalate, saying, Tommasi l’ha fatto a Noi, e Noi lo faremo a lui. (“What Tommasi did to us, we will do to him.”) It was promptly refused, and the whole day was spent in discussion between Don Tommasi and the high ecclesiastics. Eventually he wrote the pope a grateful letter of thanks, “representing to your Holiness the obstacles and impediments, my grave sins, my passions ill-controlled, my ignorance and want of ability, and my conscience bound by vows never to accept any dignity, which make it imperative to implore from your Holiness the permission to refuse the honour”. This letter was read to the Congregation of the Holy Office, and Cardinal Ferrari was deputed by Clement to tell Tommasi that the same reasons applied to him as to the pope, whom he had urged to accept the still more onerous burden of the papacy. Being finally persuaded that it was the will of God, he submitted, saying, Oh via! sara per pochi mese (“ Well it will only be for a few Months”), and went to receive the hat from his Holiness. He wrote to Maria Crocifissa to implore her prayers, saying that Saul among the prophets fell terribly, and that Judas was an apostle and perished.

Joseph Tommasi continued his simple life, going to choir with his brethren, and as much as possible avoiding all ceremony. The members of his household were dressed as poor people; amongst them was an old beggar, a converted Jew. His food was of the plainest, and even of that he ate so little that his doctor remon­strated. The new cardinal took the title of San Martino ai Monti, remembering that he had left home to begin his religious life on St Martin’s day, and also because it had been the title of St Charles Borromeo, who was his great pattern in his life as cardinal. He found it necessary to leave his monastery in order to live near his church, which belonged to the Carmelites, with whom he frequently joined in their offices as one of themselves. People flocked from all over Rome to be present at his Mass, whereat he allowed nothing but plainsong, accompanied by the organ only. At the classes of Christian doctrine on Sunday he himself instructed the smallest children, explaining the catechism and singing hymns with them. Owing to the extreme moral laxity of the day, he, with the pope’s approval and following the example of Borromeo, insisted on the separation of the sexes in the church and in approaching the altar. This raised a storm of opposition and abuse, but he persevered quietly in what he thought to be right.*{ * Separation of men from women at public worship is normal in most parts of the East, and is considered theoretically desirable in the West too: cf. the Code of Canon Law, canon 1262, § 1.}

On Christmas Eve he was very ill, but insisted on attending the services at St Peter’s, and offered his three Masses in his own chapel. He suffered greatly from cold, and, refusing all food, could only sit crouching over the fire. After two days he took to his bed. Hearing the lamentations of his famiglia and of the poor people who were crowding into the lower part of the house, he sent them word that he had asked the pope to provide for them. At times he was delirious, but his confessor repeating the name of Jesus he recovered consciousness at once. He would not have the prayers for the dying said until he asked for them. Very shortly before his death he received viaticum, and thus strengthened by the Lord he had so dearly loved, he passed quietly through the janua caeli of death on January 1, 1713. Even before his death the sick were healed through touching his clothing, and when the end had come cures multiplied round his bier. Bd Joseph Tommasi was beatified in 1803.