The church was originally built in the 1100s as a modest stone building with a west tower, measuring around 12 by 7.5 metres. At that time nuns settled nearby, living a monastic life connected to the church, which served both as a parish church and a convent church. A low, now blocked-up doorway in the south façade, known as the "nun's door", is said to recall this period.
In the 1200s the chancel was enlarged to serve the nuns' choir services, apparently under a master mason trained in the Cistercian tradition, as the masonry suggests. Before long, however, the nuns left for a newly built convent on the shore of Mälaren, Vårfruberga kloster, and the older monastic buildings beside the church were abandoned.
From then on Fogdö functioned solely as a parish church. During the 1300s and 1400s the nearby manors of Bergshammar and Hesselbyholm supported further embellishment, adding wall paintings, a new east façade, vaulting and a taller tower. A tower spire followed in the 1500s, along with coloured glass in the east window bearing the arms of the councillor Bengt Nilsson (Färla).
In the 1600s a burial chapel was added on the south side for the Posse family of Bergshammar, commissioned by the widow Catharina Elisabeth Kurck, along with a new sacristy. The roof of this burial chapel was altered in the 1800s, and the church's present entrance, in the tower, dates from 1889.
Inside, visitors can see medieval wall paintings attributed to the so-called Fogdö Master, from the early 1400s, together with a wooden triumphal crucifix and carved figures including a bishop and a mounted Saint Martin of Tours, works associated with workshops in the Mälaren valley and, in one case, Gotland. The pulpit dates from 1642, with box pews from the same century. The church also has an organ with origins in the eighteenth century, substantially rebuilt and altered several times since.