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This very old church is first remembered by a plaque, placed on the right as soon as you enter, recalling the day of its consecration (25 March 1090) by Pope Urban II, and its name ad pineam (i.e. near the pine cone). The current appellation has an uncertain origin, and there are several interpretations:

the most complex, and also the least probable, refers to the very tombstone at the entrance, the quarto stico of which reads: 'que appell(atur) ad pinea(m) per ep(iscop)os Ubaldu'; the expression que appell ad, became in popular jargon chapel;
others (Nibby, Hulsen) believe that the nominative chapel derives from the Latin cupella, i.e. barrel; proof of this is the fact that in the 15th century the Company of Barrelmasters had its headquarters in this church;
The simplest solution instead traces the name back to a pre-existing chapel or oratory on the site of the present church.
The church is then not mentioned much in the centuries following the 11th century. Apart from the consecration of an altar in 1113, the church is remembered when, for reasons of stability, the right aisle was closed to the public and in 1391 Andreozzo Ponziani, father-in-law of Francesca Romana founded the Hospital of the Santissimo Salvatore there after restoration. After his death, the hospital remained in Francesca's care and the church then passed to the Oblate di Tor de' Specchi, who gave it to the Company of Barilari in 1540.

The Doria-Pamphilj exercised patronage over it, and Innocent X gave the property in 1650 to Donna Olimpia, who, by purchasing various lands around it, had a garden of delights built, known as "i bagni di Donna Olimpia", directly overlooking the Tiber: the façade can still be seen from the Lungotevere Ripa, behind a modern wall.

Later the church became dilapidated, was closed and then reopened, then changed hands several times, until in 1797 it underwent a first series of major restorations by the Sodalizio dei Marinari di Ripa e Ripetta. Further restorations were undertaken by the Doria-Pamphilj owners in the mid 19th century, under the direction of Andrea Busiri Vici. With these works, the church took on its current appearance, and two new buildings were built on either side of the casino, installing a hospice (still functioning as the 'rest home of the Foundation of St Francesca Romana', in agreement with the public health service), and maintaining the garden.

The church façade was restored by Busiri Vici, while the bell tower is still the medieval one (12th century). The interior has a nave and two side aisles, divided by ancient columns, i.e. recovered from other previous buildings. The interior decoration is the result of 19th-century restoration work and almost nothing medieval remains. The church courtyard leads to the hospice.