The church's oldest part, the chancel, was raised in the late twelfth century using unhewn stone. Local tradition holds that twelve farmers and their families built it, and that the site had earlier been a pagan cult place before the church was established here, close to the Alnösundet strait where a defensive tower is also said to have stood. The church is dedicated to the archangel Michael.
The porch and sacristy were added in the 1400s, along with wall and ceiling paintings from the same period that are considered among the finest of their kind in Sweden. These depict figures including Saint Clement and Saint Anthony, along with a scene referring to the biblical Book of Job. A wooden sculpture of the Madonna and a triumphal crucifix, thought to predate the Swedish Reformation of 1520, are traditionally attributed to the carver Haaken Gulleson of Enånger; the sculpture is said to represent Saint Anne carrying the Virgin Mary. The current pulpit and altar rail date from 1656. The wooden porch facing the churchyard was added in the late 1700s, and the windows were altered in the same century.
A notable survival from the church's earliest period is the Alnö font, an unusual wooden baptismal font that now stands in Alnö nya kyrka and remains in use there.
By the mid-1800s the old church had become too small for the growing parish, and a new wooden church was built nearby in 1861–63. That building burned down in 1888, and a brick church, Alnö nya kyrka, was built on the same site and consecrated in 1896. The old church then stood empty for around three decades before restoration work began in about 1930, after which it returned to occasional use.
Today Alnö gamla kyrka is used by the parish for special occasions and remains a sought-after venue for weddings, with seating for around 75 people.