The church was completed around 1150, its walls built from sandstone quarried on southern Kinnekulle. The apse and nave walls surviving from this period give the building its Romanesque character. From the same era comes the font, carved by a craftsman named Othelric, whose reliefs depict the struggle between Christianity and paganism and are regarded as among the finest in Västergötland.
Several medieval wooden sculptures once housed here, including a triumphal crucifix, a figure of the Virgin Mary and one of the Archangel Michael, have since been moved to museum collections in Skara, while a seated oak Madonna figure known as the Skebymadonnan, carved in the early 1200s, is kept at the Västergötland Museum. In the church's early centuries there were no pews, and light entered only through small windows on the south side.
A tower was added in the early 1500s, replacing an earlier freestanding bell-frame in the churchyard, though its upper section was burned by Danish forces in 1566. The building was altered again in 1796, when the chancel wall was raised and the nave and chancel given a shared timber roof and ceiling.
Around 1700 the church underwent substantial repair, gaining a gallery and a new pulpit, and it was during this period that the painted decoration still visible today was applied. The present tower dates from 1828, and heating was not introduced until 1885, with a wood-burning stove and inner windows.
A pulpit-altar, a combined furnishing rarely found in Swedish churches, was installed in 1961, giving Skeby kyrka one of its most distinctive features today. The organ, built in 1894 by Carl Axel Härngren and enlarged in 1977, remains a modest instrument of one manual and pedal.