During the past five years of excavations on the island by a team of archaeologists led by Dr. David Caldwell of the National Museums of Scotland, much has been learned about the various buildings and the way of life of the people who used them. Evidence of fortifications, a great hall, extensive living quarters, a chapel and paved roads, proved the island had indeed been occupied by a rich and sophisticated people.
The defences surrounding Eilean Mor were never replaced in stone, but before it was possible to bring artillery to bear against such an island fortress, earth embankments with timber fortifications could be very effective.
The chapel was dedicated to St. Findlugan and situated on a limestone outcrop, the prime site on the island. In earlier days the island was smaller than today. Alluvial tails have built up at the northern end. Over the years the construction of buildings and roads caused further accumulation of ground.
During the first year of excavation a road was uncovered leading from the jetty on the west side of the island towards the chapel, and in succeeding years a network of roadways has been uncovered.
It is assumed that an early Christian monastery was established by the early Irish monks. Huts mainly of wood and thatch surrounded by a ditch were the established form of the early Irish monastic communities.
Limited excavation to date has shown that the Council Island is mostly artificial, an accummulation of ruined buildings from different eras.
The tombstones probably lay on the floor of the Chapel until the late 19th century when there was amateur digging. Tombstones were traditionally those of wives and children of the Lords of the Isles, who were themselves buried in Iona. There is certainly one child-size tombstone.
The effigy of a warrior wearing an aketon or quilted overgarment is almost certainly on the tombstone of MacGilleasbuig of Finlaggan who died after the forfeiture of the Lordship. This family seems to have been of considerable standing even before the forfeiture, and after it they became the chief family at Finlaggan.
Very little remains of the Great Hall which was the largest and most important secular structure on the island. used for feasting and social entertainment. It was well built, mortared, the lower courses of the walls built wide for support, forming an impressive hall with a large fireplace and slate roof. The doorway is of considerable interest archaeologically with nonmatching jamb stones of carved sandstone suggesting reconstruction of the original building.
After the hall fell out of use as a roofed structure, it was massively robbed of stonework. This was no gradual process but an organised dismantling of the complete structure.
One of the first discoveries in the graveyard during excavations in June 1990 was the head of a typical example of a West Highland freestanding cross carved in Iona workshops in the 14th or 15th centuries. The shaft has not yet been found.