There are many rune stones in the church walls and in its vicinity. This suggests that a wooden church was built on this site during the later part of the 11th century.
About 100 years later, the tower and nave were built, which are the original parts of the present Spånga kyrka. At that time the church was also probably used for defensive purposes, as its walls suggest this.
The original window openings on the south and north sides were closed up during the first half of the 14th century, and new openings were made on the south side. The limewash paintings with ornaments, some of which still decorate the vault ribs, were probably added at the same time as the church interior was vaulted. The figurative painting in the vault webs is estimated to date from the 1440s.
The original chancel was demolished and a new, larger one erected in the same position during the mid-15th century, and the church porch on the south side was built. The decorative limewash paintings were probably added when these parts were built.
During the 1670s the Bonde family burial chancel was erected. At that time, the Bonde family of Hässelby slott were the major landowners in the area. The burial chancel was built for the Lord High Treasurer, Baron Gustaf Bonde, who died in 1667, and Nicodemus Tessin the Elder was probably the architect.
Between 1953 and 1955 an extension was made on the north side of the church, along with an extensive renovation of the interior. The architect was Erik Lundberg (1895–1969), one of the most influential restoration architects of the 20th century. He wanted to restore as much as possible of the medieval "architectonics", which, among other things, led to the medieval limewash paintings, which had been painted over in 1905, being uncovered again.
Spånga kyrka is a very important link between the area's earliest history and today's society, through the rune stones, medieval walls and limewash painting, the burial chancel of the late 17th century, the buildings of the 18th and 19th centuries in the immediate surroundings, and its place in one of today's Stockholm suburbs.