The ruin consists of grey stone wall fragments lying west of the Värdshuset inn and close to Skokloster Castle, roughly a kilometre north-west of Skokloster Church in what was Skokloster parish, Håbo hundred. The church was built during the first half of the twelfth century in the typical Romanesque plan of the period: a nave and a narrower chancel ending in a semi-circular apse, with a tower to the west. An extension on the south side of the chancel has an unknown original purpose, though it has been suggested it may have served as a burial chapel for a noble family. The site of the old, now abandoned churchyard lies just outside the ruined walls.
In the 1230s, Cistercian nuns are said to have travelled from Byarum Abbey in Småland to this part of Uppland, and it is thought their first dwellings were established here, close to Flasta's old parish church, which may then have briefly served as their earliest monastic church. This connection between an ordinary parish church and an incoming religious community is one of the more distinctive aspects of the site's history, though the details rely on limited documentary evidence.
Work on Skokloster Church and its associated monastic buildings began in the 1240s on the eastern shore of the Sko peninsula, and the new church's altar was consecrated in 1288. Flasta's old church is said to have burned down a few years later, after which regular use of the building ceased and it fell into ruin.
Archaeological excavations carried out at the site in 2006 uncovered a number of items of interest, including a fragment of a medieval font bowl decorated with relief carving showing trailing plant tendrils together with parts of a stag and a lion. A woman's grave within the excavated area yielded two oval brooches and a neck ring, and an unusual belt-end fitting decorated with enamel was also found within the ruined walls.