The family had moved into the southern Italian province of Apulia, where Padre Pio lived. Stefano was visited from the 8th December 1945 at the age of 12 years, the minor seminary of Cupertino. He entered the Friars Minor, and took simple vows on 4 October 1949, which on 27 May 1954 was followed by solemn perpetual vows. On 30 October 1955 he was consecrated at Christ the King, a particularly precious feast to him as a priest.
In 1960 Father Stefano received his doctorate at the Seraphicum, the Pontifical Faculty of Theology in Rome, with a thesis on the Immaculate Conception. The work explains the choice of his community's name. He then followed by teaching Patristics and Mariology at the convent's seminaries at the Archdiocesan Seminary of Benevento and the Institute of Religious Sciences of Avellino. From 1982-1988 Father Stefano Maria was twice provincial of the Order of Friars Minor of the Province of Naples.
Around 1965 a gradual rediscovery and long observation of the Franciscan sources and the writings of the Saint Maximilian Kolbe began for Manelli.
The call of the Second Vatican Council, to return to the sources of religious renewal and adjust the proclamation of faith to the changed circumstances of the time, led Father Stefano Maria to a new Franciscan-Marian Journey.
On 24 December 1969 Father Stefano Maria and his brother, Father Gabriele Maria Pellettieri asked the Superior General of the Friars Minor for the permission to lead a renewed, more rigorous Franciscan life, which was tied into the foundation. A Franciscan-Marian manner of life they called the "Marian traces of Franciscan life." The result was in the first Marian House in August 1970 at the Marian Shrine of Our Lady of Good Counsel in Avellino Frigento.
Over the years, the two brothers grew more and more inspired by the ideal of evangelical radicalism. This increase, the special charism, the consolidation of a particular manner of life, and other opposing trends in parts of the Mother House led the Order, after 20 years on 22 June 1990, to the establishment of a separate order. The Church's recognition of diocesan right was professed in a corresponding decision by Pope John Paul II, through the Archbishop of Benevento, Monsignor Carlo Minchiatti. On 1 January 1998 the recognition of the Order was established by papal law. A special feature has been added to the three traditional religious vows poverty, chastity and obedience, a fourth vow, the unconditional consecration to the Immaculate Virgin Mother of God.
On 1 November 1982 Father Stefano Maria and Father Gabriele Maria, founded the first community of Franciscan Sisters of the Immaculate in Novaliches, Philippines. The female branch, which was passed in its inception phase was led by Father Gabriele Maria Pellettieri, lives according to the same Franciscan-Marian ideal of the brothers. As of 2013 there are more than 50 branches of the Franciscan Sisters on all continents. The Order has more than 350 sisters.
In 2006 the youngest of the family followed with the Order of Poor Clares, a contemplative branch of the Immaculate Conception, which includes today four cloistered convents with more than 40 sisters.
On 8 September 1990 there followed - alongside the male and female religious branches - the establishment of a lay association, the Mission of the Immaculate Mediatrix (MIM). The laity living the religious ideals in their respective state and various stages of Consecration to the Immaculate Virgin Mother of God (Missionaries of the Immaculate Conception with consecration, Missionaries of the Immaculate Conception with a private vow as Franciscan Tertiaries of the Immaculate Conception).
In 2008, the General Chapter undertook the decision to return as a community to the traditional form of the Roman Rite rehabilitated by Pope Benedict XVI in the motu proprio Summorum Pontificum as an extraordinary form of the Roman Rite and returned to the Church.
As of 2013 (prior to the crisis) the Franciscans of the Immaculate are now represented on all five continents. The order counts all together, some 650 members of religious orders have stirred an increase in vocations. They promote the Tridentine Rite and go to the street and around the world as missionaries. Since 23 June 1990 Father Stefano Maria Manelli has been Minister General of the Franciscans of the Immaculate, whose Generalate is in Rome.
Following the Decree of the Congregation for Institutes of Consecrated Life and Societies of Apostolic Life of 11 July, 2013 (Prot. N. 52741/2012), that placed the Capuchin Father Fidenzio Volpi as Commissioner of the FFI, Fr. Stefano M. Manelli, with the entire Institute of the Franciscans of the Immaculate united with him, obeyed the Holy Father's decision and trusted that with this obedience there may come even greater graces.