As the Diocese of Surigao grew at the turn of the century, a plan to put up its own seminary was made. On 1958, Msgr. Carlosvan den Ouwelant, MSC, started the seminary's construction at the outskirts of Butuan. It was finished the year after and was consecrated to St. Peter the Apostle, the first diocesan priest. It opened as a high school seminary administered by Belgian CICM missionaries.

When the Diocese of Butuan was created in 1967, Msgr. Carmela D.F. Morelos stood as its first bishop and the seminary began to cater to seminarians from both dioceses of Butuan and Surigao. Nine years later, Bishop Morelos spearheaded the opening of a
college seminary which welcomed the seminary's high school graduates as well as graduates from the neighboring Urios College. The high school was gradually phased out in 1977 as the institution focused its energies in producing college-level seminarians. That same year, its last Belgian CICM rector, Rev. Fr. Carlos Lindemanns, turned the seminary over to the diocesan clergy with Rev. Fr. Bienvenido Betaizar, its first Filipino diocesan rector.

St. Peter College Seminary (SPCS) became a sub-regional college seminary under the care of the bishops of the dioceses of Butuan, Surigao, and the newly formed Diocese of Tandag in 1978. The seminary inaugurated its pre-college department in 1984, and
was given recognition by the Commission on Higher Education as an independent, degree-granting institution in 2006. After celebrating its 55th year of service to the Church in 2014, SPCS continues to provide formation for future ministers from the
dioceses of Butuan and Tandag. It is proudest of the 145 ordained clergy and the hundreds more of God-fearing men it has produced over its long history.

​