Benozzo spent time in the capital of Christianity on three separate occasions.
In 1447, he worked with "il Beato Angelico" (the Blessed Angelic One) on the decoration of the Cappella Maggiore of Saint Peter, in the Vatican City. Pope Eugene IV had had the opportunity to admire the work of these two painters during his earlier stay in Florence and therefore commissioned this prestigious cycle of frescoes of which, sadly, nothing now remains. For this reason, it is not possible to identify the young Benozzo’s role in their creation.

However, the frescoes (also painted in partnership with Angelico) commissioned in 1448 by the newly elected Pope Nicholas V for his Niccoline Chapel in the Vatican Palace, depicting the Stories of the Deacon Martyr Saints Stephen and Lawrence, have survived. In view of Benozzo’s proven experience at Fra Angelico’s side and given the substantial payments, of which documentation still survives, the part he played in the painting of these decorations must have been significant.

Other works documented by sources and produced during this stay in Rome appear to have been lost, with the exception of the processional standard of the Madonna and Child under a canopy, painted for the Basilica of Santa Maria Sopra Minerva.

Benozzo then returned to Rome in 1453 and, the following year, decorated the chapel of the noble Albertoni family, one of the most important family chapels in the Church of Santa Maria Aracoeli. Of these frescoes, only the Saint Anthony of Padua and donors, painted on the wall behind the altar, now survives. In the meantime, Angelico had also returned to Rome where he succeeded in completing his final works before his death in 1455. Benozzo, the undisputed heir of his master and partner, was commissioned to paint the Sapienza Nuova Altarpiece by Benedetto Guidalotti, then the Bishop of Perugia, for whom Angelico had previously painted a beautiful polyptych for his family altar. Benozzo carried out the work in Rome and sent it to Perugia. It can be seen today in the National Gallery in Umbria together with the panel painted by "il Beato Angelico" (the Blessed Angelic One) for the same client.

Another work attributable to this period is the fine panel painting of the Collegiate Church of Sermoneta depicting the Madonna and the angels