The current complex is composed of the church, the monastery, and a brickwork bell-gable.

The interior of the single-nave church still preserves traces of the preceding structures, particularly in the square-plan crypt which holds some column capitals sculpted in styles which date from before the 11^th century. The crypt's groin-vault ceiling is reinforced by a central pillar.

Many episodes from the life of Saint Francis are connected to the abbey. The saint's biographers tell of how Francis sought refuge here after having been attacked near Caprignone; the prior, however, did not receive him well, and the saint was charged with lowly housekeeping tasks. Years later, the abbey's prior went back to Francis to beg for his forgiveness; from then on, during his frequent pilgrimages to La Verna, Francis was often hosted at Vallingegno.

It is also said that in the monastery's stables, Saint Francis was moved by the death of a small lamb who'd been killed by the bite of a cruel sow, and cursed the animal, who died after three days of agony.