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In 1803 Elizabeth, William Magee Seton, and their oldest daughter Anna Maria sailed to the warm climate of Italy, in a desperate effort to restore her William's health. Italian authorities at the port of Livorno feared yellow fever then prevalent in New York. As a result, the Setons were quarantined in a cold, stone San Jacopo lazaretto. The Filicchi family did all they could to advocate for them and to provide some relief during their month of isolation. Two weeks after his discharge, William Magee Seton died in Pisa on December 27, and was buried in the English cemetery in Livorno, leaving Elizabeth a widow at age twenty-nine with five young children.
The experiences in Italy transformed the lives of Elizabeth and her daughter (now named Annina). Antonio Filicchi (1764-1847) and his wife, Amabilia Baragazzi Filicchi (1773-1853) provided gracious hospitality to the widow and child until the Setons returned to the United States the next spring. Filippo and his wife, the former Mary Cowper (1760-1821) of Boston, along with Antonio and Amabilia Filicchi, introduced Elizabeth to Roman Catholicism. Elizabeth came upon the text of the Memorare. Her lack of knowledge about the religion and inquisitive nature led her to inquire about the Catholic practices. She asked about the Sacred Liturgy, the Real Presence in the Eucharist, and the Church's direct unbroken link with Christ and the apostles. The Italian Journal, her long memoir written for her sister-in-law Rebecca Seton, reveals the intimate details of Elizabeth's heart-rending personal journey of inner conflict and conversion (cf. Collected Writings, 1:243). Antonio, who had business interests in America, accompanied the Setons back to America, and instructed Elizabeth about the faith and offered wise counsel during her indecision. Elizabeth felt deeply for Antonio, who provided not only emotional support but also substantial financial resources to her.
Although Elizabeth left the United States a firm Protestant, she returned to New York in June 1804 with the heart of a Roman Catholic. Immediately, opposition and insecurity threatened her resolve. Elizabeth's religious inclinations incurred the ire of both family and friends. Their hostility, coupled with the death of her beloved Rebecca, her sister-in-law and most intimate confidant, caused Elizabeth deep anguish. She was also troubled by her strained financial situation. Her five children were all less than eight years of age. As their sole parent Elizabeth faced many challenges and frequently had to relocate into less expensive housing.
While Elizabeth was discerning God's will for her future, the Virgin Mary became her prism of faith. In her discernment she relied on several advisors among the clergy, Rev. John Cheverus (1768-1836) and the first bishop of Boston, and his associate Rev. Francis Matignon (1753-1818). Struggling with doubts and fears in her search for truth, Elizabeth resolved her inner conflict regarding religious conversion and embraced Roman Catholicism.
 On March 14, 1805 Reverend Matthew O'Brien (1758-1815) received Elizabeth's profession of the Catholic faith at Saint Peter's Church, Barclay Street in lower Manhattan. Elizabeth received her First Communion two weeks later on March 25. Bishop John Carroll (1735-1815, later archbishop), whom she considered her spiritual father, confirmed her the next year on Pentecost Sunday. For her Confirmation name Elizabeth added the name of Mary to her own and thereafter frequently signed herself "MEAS," which was her abbreviation for Mary Elizabeth Ann Seton. Accordingly the three names, Mary, Ann, and Elizabeth, signified the moments of the mysteries of Salvation for her.
Elizabeth's initial years as a Catholic (1805-1808) in New York were marked by disappointments and failures. Rampant anti-Catholic prejudice prevented her from beginning a school. She eventually secured a teaching position at the school of a Protestant couple, Mr. and Mrs. Patrick White, but they failed financially within a short time. Elizabeth's next venture was a boarding house for boys who attended a school directed by Rev. William Harris of Saint Mark's Episcopal Church, but disgruntled parents withdrew their sons. Seton family members also distrusted Elizabeth's influence on younger family members. Their fears were realized when Cecilia converted to Catholicism (1806), and followed by Harriet’s profession of faith (1809). During Cecilia's struggles as a new convert, Elizabeth wrote an instructive Spiritual Journal (1807) for her, offering her wise counsel.
Although Elizabeth was frustrated in establishing herself to provide for the welfare of her children, she remained faith-filled. She was convinced that God would show her the way according to the Divine Plan. In considering her future and examining alternatives, Elizabeth remained a mother first and foremost. She regarded her five "darlings" as her primary obligation over every other commitment.
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