In 2004, a new building was built at Koper Prison, which was the first such investment in the prison system for 40 years. A modern prison was built which meets the prescribed standards. Before this, Koper Prison operated in the Franciscan monastery of St Anne, which was returned to its owner in 1997 on the basis of denationalisation proceedings, and it was used on a lease contract until the new prison was built.

The prison has a closed, semi-open and open unit for convicted men, and a detention unit. Imprisoned men are accommodated in 72 rooms, of which 32 are single and 40 are double rooms. Other rooms are also available for the imprisoned men: common living rooms with a kitchenette, a dining room, workshops, reception areas, rooms for visits, a room for spiritual care, several smaller rooms for exercise, a gym, three indoor walking areas, an outdoor sports field, a room for education and other leisure activities, a library, a general and dental clinic, a hospital room, a room for the disabled, a special room for exclusion, a room for disciplinary punishment of a solitary confinement, a convenient shop, a hairdressing room and technical and auxiliary facilities, such as a laundry room, a room for ironing and a storage room for clothes and bedding.