The site is thought to have been first built around 1200, though little is known of that earliest church beyond what excavations in 1927 revealed: a cross-shaped plan with a narrower eastern chancel and, intriguingly, a round structure between the north transept and chancel that has been interpreted as a side chapel or grave chapel connected with the cult of Helena. A larger Romanesque church followed, later extended into a three-aisled building with transepts in the 1200s, possibly modelled on Gudhem's convent church, and further altered around 1400 when the chancel was enlarged and a tower added.
As a pilgrimage church associated with the grave of a locally venerated saint, S:ta Helena drew considerable numbers of visitors in the Middle Ages, and the parish was reputedly among the wealthiest in the diocese. The building suffered repeated fire damage, notably during Danish campaigns in 1566 and 1611, and again in 1624 and 1759, after which it was rebuilt with a new three-sided chancel.
The church's present appearance owes much to later restorations. Carl Möller's work, completed in 1888, widened the transepts, removed the Baroque interior, exposed the roof timbers and gave the tower its slender neo-Gothic spire; the facades were rendered with quarry-stone patterning, pointed windows and buttresses. Axel Forssén's 1927 restoration swept away Möller's interior in favour of a vaulted ceiling in a late-Baroque idiom. The most dramatic change came in 1972, when Yngve Tegnér's modernist restoration created an entirely new interior, working with artist Olle Nyman; a suspended aluminium acoustic ceiling, decorated by Nyman and shaped as a cross evoking Christ's resurrection, remains a striking feature. Möller's exterior was deliberately retained throughout.
Only a few fragments connect the church to its earlier phases: a Romanesque sandstone portal, now in the north transept, survives from the first stone building, and a wrought-iron grille with a diamond pattern, dated to the 1400s, is said to have stood before the entrance to the saint's burial chamber; a glazed opening in the chancel floor allows a view down towards where the steps to this vault are thought to have been. A niche statuette of the saint by Astri Taube (1950) can be seen on the church's north exterior wall, and a modern sculpture by Thomas Qvarsebo, unveiled in 2017, depicts Christ at the moment of death.
According to tradition, Helena (also called S:ta Elin) was a wealthy, devout widow from Våmb who devoted herself to charitable works and was murdered near Götene after being blamed, seemingly unfairly, for her son-in-law's death at the hands of her household servants. She was canonised in 1164, reputedly Sweden's first female saint, and is credited with founding this church as well as those at Våmb and Götene. The church has had several organs over the centuries, including instruments from 1769, 1865, 1951 and the present one installed in 1974.