It is believed to have been built when the town was of strategic importance to the Christian kings of Castile in their defence against Moorish invaders; the church is situated on an imposing hill below a fortified castle.
The apse was eventually exchanged in a complex deal that involved the gifting by New York of six frescoes from the San Baudelio de Berlanga to the Prado Museum, on an equally long term loan.
They include, in its dome, a large fresco c. 1130–50, from the Spanish Church of Sant Joan de Tredòs, in its colorisation resembling a Byzantine mosaic and is dedicated to the ideal of Mary as the mother of God.
In the early 1930s, the philanthropist John D. Rockefeller Jr., who had commissioned The Cloisters, financed the Metropolitan Museum of Art to acquire a number of Medieval architectural elements from Europe for incorporation into the building.
Representatives were sent to Europe, mostly to France, to find an apse that might be suitable, with the current one from the San Martín Church, Fuentidueña identified in 1931, shortly after it had been declared a Spanish National Monument.
It was built in the mid 12th century, when the town was of strategic importance to the Kingdom of Castile, then defending against the Moors; it is situated on a hill, somewhat imposingly, and just below a castle, for which it probably served as its chapel.
[12] The exchange was looked upon more favorably by the Spanish 12 years later, when again approached by the Metropolitan, who argued that the apse would be better conserved in a roofed building.
During the negotiations, the Spanish were represented by Francisco Javier Sánchez Cantón (later director of the Prado), and the archaeologist and historian Manuel Gómez-Moreno Martínez.
The Metropolitan assured the citizens of Fuentidueña by promising to pay for the reinforcement of the local parish church of San Miguel, and to rebuild its tower, which was then also in disrepair, and threatening to fall.