Spiritual Formation is at the heart of every vocational journey. At Scotus College, spiritual formation permeates all aspects of formation. Specific elements in spiritual discernment include: the Eucharist, Personal Prayer, Reconciliation, Spiritual Direction, Retreats and Recollection, Spirituality Classes, Pilgrimages and Communal Liturgy.

Eucharist is celebrated daily in the College chapel, where Morning and Evening Prayer are also recited in common. In addition to the chapel, there are two oratories designed for private prayer, and these are also used for rosary and night prayer. There is Exposition of the Blessed Sacrament with Benediction on Sunday evenings.

Father Angus MacDonald, the Spiritual Director, is responsible for the individual Spiritual Direction of the students, and for the Spirituality classes. Retreats are led by a variety of presenters, who encompass the rich traditions of spirituality in the Catholic Church. Each year several retreats are held in house, and one takes place at a chosen retreat centre. This allows the students to participate both in preached and thematic retreats, and in individually guided retreats.

During the seasons of Advent and Lent, the College Community particpate in Lectio Divina together. These seasons are also marked by Reconciliation Services, which are led by invited local priests, both diocesan and religious.

The College community particpate in an annual pilgrimage, which is seen as one of the central spiritual exercises of the year. Recent years have included pilgrimages to the Church of St Blane on the Isle of Bute, to the cave of St Ninian at Whithorn, and to the scottish seminary traditions found in Morar.

First year students are encouraged to encounter a variety of styles of prayer by participating in the "Reflective Living Course" run by the Ignatian Spirituality Centre.