The oldest surviving part of the building is the western section of the nave, dating from the 12th century, when a tower-less stone church with a small square chancel was built. During the 14th or 15th century the original chancel was demolished and the nave extended eastwards, following a common pattern of the period, creating a hall-church form. A sacristy was added north of the new chancel, along with a porch to the south, and brick vaults, including a star vault over the chancel, were built into the interior towards the end of the 1400s.
In the 17th century the church was extended further east, a project funded by the officer and governor Gustaf Cruus af Edeby, who also established a burial vault for his family beneath the new chancel. Several members of the Cruus and related Fleming families are said to be buried at Helgarö.
A serious fire in 1686 (sources differ on the exact year, with one giving 1681) destroyed much of the church's fittings, including the altarpiece and pulpit. The building was reconstructed with the help of donated funds and a national collection, reopening a few years later. A west tower and the present sacristy were added in the 18th century.
The 19th century brought extensive restoration: the roof covering was replaced with tiles in 1864, and a new neo-Gothic west tower, designed by the architect Emil Viktor Langlet and built to carry the bells, was completed in 1886. A further interior restoration in 1898 introduced medieval-style decorative paintings on the vaults and walls, as well as the organ façade seen today.
Among the church's notable furnishings is an altarpiece depicting the Last Supper, painted by the court painter Georg Engelhard Schröder and donated in 1735 by Maria Christina Fleming of Edeby; its elaborate Baroque-style frame was added during the 1898 restoration. The late-Baroque pulpit dates from 1741, with its original marbling and gilding uncovered during a 1957 restoration, when the current pews were also installed. The font was carved by the Strängnäs sculptor Erik Sand in 1957. The present organ, built in 1915 by E A Setterquist & Son of Örebro, replaced two earlier instruments and was renovated in 1984.