The church's round form is unusual in Swedish ecclesiastical architecture; only a handful of round churches were ever built in the country. A papal letter of 1185 confirmed that Sweden's archbishop had received land at Munsö from King Knut Eriksson, and the archbishop periodically resided nearby at Bona, the manor just east of the church. This round design is generally linked to a tradition of building inspired by the Church of the Holy Sepulchre in Jerusalem and Charlemagne's palace chapel at Aachen, though such attributions for round churches are often more symbolic than documented.
The building developed over several centuries. A sacristy was added to the north in the fourteenth century, and a porch was built to the south in the fifteenth century, though its brick vault followed somewhat later. In the 1470s a dome-like vault was constructed within the round nave, possibly following a fire. A detached wooden bell tower was raised southwest of the church in the 1720s.
Inside, the round nave has long been read as carrying deliberate Christian symbolism: its circular shape is traditionally interpreted as representing eternity and the encompassing love of God, while the interior overall has been described as evoking contrasts between light and dark, heaven and earth, life and death. The oldest surviving object in the church is a font dating from the thirteenth century.
The church's organ was built in 1838 by the noted Stockholm organ builder Pehr Zacharias Strand and was substantially restored to something close to its original condition in 1981. In the eighteenth century, the antiquarian Johan Peringskiöld claimed Munsö kyrka was Sweden's very first church, supposedly founded by a chieftain converted by the missionary Ansgar in the ninth century — a colourful tradition that later historians treat with considerable caution.