The dedication itself is unusual: few medieval Swedish churches were named for the Holy Trinity, suggesting the parish's origins lie in the early Middle Ages. The present building is thought to be the third church on this site, with its sacristy dating from the late thirteenth century and the main three-aisled basilica raised during the fourteenth century, built of granite in its lower courses and brick above. The church is first recorded by name in 1302 and has also been known locally as Bondkyrkan.
The sturdy but low tower was added towards the end of the medieval period, possibly in the fifteenth century; its original tall spire was destroyed in the great Uppsala fire of 1702 and replaced with the present dome-like cap. On the tower's south side survives a heavily restored medieval sundial, calibrated to Swedish winter time. Inside, the vaults and the walls of the Mary Chapel bear fifteenth-century paintings attributed to Albertus Pictor, later whitewashed in the eighteenth century, uncovered again in 1905, and subsequently cleaned and conserved several times during the twentieth century.
A drastic renovation in 1802 saw almost all the medieval fittings sold off, including the altar, altarpiece, pulpit and font; only three wooden sculptures from that period remain, now placed above the sacristy door. The current pulpit dates from 1905 and carries an inscription added by Nathan Söderblom, who served as the parish's vicar for thirteen years before becoming Archbishop of Sweden. Behind it stands an unusually tall chair, said to be perhaps 300 years old, once used by preachers. The present font, thrown in ceramic, was donated in 1981 by the Uppsala Ekeby pottery works on the occasion of its closure.
Other notable furnishings include a portrait of Nathan Söderblom by Louis Sparre in the south choir, and early twentieth-century stained glass depicting figures such as Saint Birgitta, Gustav II Adolf and Johan Olof Wallin. A memorial stone from Nidaros Cathedral in Norway was given in gratitude for the parish's support of Norwegian refugees during the Second World War. The church's two bells, cast in the nineteenth century, still hang in the tower.
The organ has a layered history: earlier instruments from the seventeenth, eighteenth and nineteenth centuries were rebuilt or replaced over time, and a 1905 organ was destroyed by fire. The current mechanical organ was built in 1993 by Robert Gustavsson's workshop, with a façade designed in 1991 by Ulf Oldaeus, and stands in the north side choir; a smaller, older chamber organ, possibly dating to the early 1800s, occupies the north side of the chancel.