The church began as a simple nave, to which a porch and sacristy were added during the 14th and 15th centuries. In 1450 the original timber ceiling was replaced with brick vaulting, giving the interior its current character. Above the nave survive 26 medieval roof trusses, thought to date largely from the 1300s, while several trusses in the porch are from the later medieval period.
Unlike many Swedish parish churches, Säby has no tower. Instead, its two medieval bells hang in a freestanding wooden bell frame built in the 18th century, standing apart from the church itself.
Among the church's furnishings is a font believed to date from around the mid-12th century, making it considerably older than the present building and presumably retained from an earlier church on the site. A carved image of the Virgin Mary dates from the early to mid-17th century, and the well-preserved pulpit was made in 1680 by the local craftsman Erik Nilsson, known as the Fläckebo joiner.
The present organ was built in 1901 by the Gothenburg firm Thorsell & Erikson, replacing an earlier instrument from 1856. It is a mechanical organ with a modest but characteristic Romantic-era specification.
The church can seat up to 80 visitors, reflecting its role as a small rural parish church rather than a grand building, though its combination of medieval fabric, later additions and well-preserved fittings gives it particular interest for visitors to this stretch of the Mälaren shoreline.