From Gregory, the powerful Count of Tusculum, father of Popes Benedict VIII and John XIX, Nilus obtained the site, which had been a Roman villa, where among the ruins there remained a low edifice of opus quadratum that had been a tomb but had been converted to a Christian oratory in the fourth century.

Building materials scavenged from the ruined villa were incorporated into the new structure, marble columns, sections of carved cornice, and blocks of the volcanic stone called peperino.

The abbey's possessions in lands were numerous and widespread, and in 1131 King Roger II of Sicily made the abbot Baron of Rossano with an extensive fief.

Between the 12th and 15th centuries the monastery suffered from the continual strife of warring factions: Romans and Tusculans, Guelphs and Ghibellines, popes and antipopes, Colonna and Orsini.

From 1163 till the destruction of Tusculum in 1191, the greater part of the monastic community sought refuge in a dependency of the abbey, the Benedictine protocaenobium of Subiaco.

In the middle of the 13th century the Emperor Frederick II made the abbey his headquarters during the siege of Rome, while in 1378 Breton and Gascon mercenaries held it for the antipope Clement VII.

The most distinguished were the Greek Bessarion, Giulio della Rovere (afterwards Julius II), and the last of the line, Cardinal Consalvi, secretary of state to Pius VII.

Till 1608 the community was ruled by priors dependent on abbots in commendam, but in that year Grottaferrata became a member of the Basilian congregation founded by Gregory XIII.

The Greek Rite which was brought to Grottaferrata by St. Nilus had lost its native character by the end of the twelfth century, but was restored by order of Leo XIII in 1881.

[6] The Abbey of Saint Mary of Grottaferrata [it] has several courts, which lead to the famous portico designed by Antonio da Sangallo the Younger, with an arcade of nine bays supported by slender columns with Renaissance capitals.

Of the abbey church consecrated by John XIX in 1024, little can be seen in the interior except the mosaics in the narthex and over the triumphal arch, the medieval structures having been covered or destroyed during the "restorations" of various abbots in commendam.