Major works of art in the church include the Apparition of the Virgin to St. Bernard (c. 1486) by Filippino Lippi (originally commissioned by Piero del Pugliese for his chapel at Chiesa di Santa Maria del Santo Sepolcro or delle Campora) and the tombs of Willa's son Hugh, Margrave of Tuscany (died 1001) and the lawyer and diplomat Bernardo Giugni (1396–1456), both by Mino da Fiesole (latter completed c. 1466).
The murals in the apse were completed by Giovanni Domenico Ferretti in 1734.

The attached Chiostro degli Aranci (Cloister of the Oranges) contains a fresco cycle (c. 1435–1439) on the life of St Benedict, rooted in the context of the Badia's revitalizing by a prominent monastic reformer of Portuguese origin, Abbot Dom Gomes Eanes (OSB) ("Beato Gomezio" in the contemporary Italian sources) (c. 1383–1459).
Many attribute the frescos to the Portuguese painter Giovanni di Consalvo, a generally unknown follower of Fra Angelico.
They are more likely the work of Zanobi di Benedetto Strozzi(1412–68) under the guidance of Angelico himself.
The fourth scene in the cycle was repainted c. 1526-1528 (St. Benedict chastising himself) by the young Bronzino.
The cloister itself was built under the direction of Antonio di Domenico della Parte and Giovanni d'Antonio da Maiano, with some assistance by Bernardo Rossellino.

The Badia Polyptych by Giotto, now at the Uffizi Gallery, was originally located in the church.
In 1940, during the safe hiding of various works during World War II, Ugo Procacci noticed the polyptych being carried out of the Santa Croce basilica.
He reasoned that it had been removed from the Badia during the Napoleonic occupation and accidentally re-installed at Santa Croce.
Procacci also realized that the altarpiece was too large for the site of the current altar at the Badia.
He discovered that a 1628 renovation had resulted in a change of the altar's location, as well as the demolishment of two and a half walls at the original site.
The remaining left half of the rear wall had been covered by a new wall.
As the polyptych was being restored in 1958, Procacci had a hole chiseled at the top of the more recent wall and found that the original wall was frescoed.
The later wall was removed over six months, and three scenes were revealed: an Annunciation, a Presentation of Jesus at the Temple and Joachim Among the Shepherds.
However, all but one head depicted in the frescoes, that of a shepherd, had been removed in the 1628 renovation.
Major works of art in the church include the Apparition of the Virgin to St. Bernard (c. 1486) by Filippino Lippi (originally commissioned by Piero del Pugliese for his chapel at Chiesa di Santa Maria del Santo Sepolcro or delle Campora) and the tombs of Willa's son Hugh, Margrave of Tuscany (died 1001) and the lawyer and diplomat Bernardo Giugni (1396–1456), both by Mino da Fiesole (latter completed c. 1466). The murals in the apse were completed by Giovanni Domenico Ferretti in 1734.
The attached Chiostro degli Aranci (Cloister of the Oranges) contains a fresco cycle (c. 1435–1439) on the life of St Benedict, rooted in the context of the Badia's revitalizing by a prominent monastic reformer of Portuguese origin, Abbot Dom Gomes Eanes (OSB) ("Beato Gomezio" in the contemporary Italian sources) (c. 1383–1459). Many attribute the frescos to the Portuguese painter Giovanni di Consalvo, a generally unknown follower of Fra Angelico. They are more likely the work of Zanobi di Benedetto Strozzi(1412–68) under the guidance of Angelico himself. The fourth scene in the cycle was repainted c. 1526-1528 (St. Benedict chastising himself) by the young Bronzino. The cloister itself was built under the direction of Antonio di Domenico della Parte and Giovanni d'Antonio da Maiano, with some assistance by Bernardo Rossellino.
The Badia Polyptych by Giotto, now at the Uffizi Gallery, was originally located in the church. In 1940, during the safe hiding of various works during World War II, Ugo Procacci noticed the polyptych being carried out of the Santa Croce basilica. He reasoned that it had been removed from the Badia during the Napoleonic occupation and accidentally re-installed at Santa Croce. Procacci also realized that the altarpiece was too large for the site of the current altar at the Badia. He discovered that a 1628 renovation had resulted in a change of the altar's location, as well as the demolishment of two and a half walls at the original site. The remaining left half of the rear wall had been covered by a new wall. As the polyptych was being restored in 1958, Procacci had a hole chiseled at the top of the more recent wall and found that the original wall was frescoed. The later wall was removed over six months, and three scenes were revealed: an Annunciation, a Presentation of Jesus at the Temple and Joachim Among the Shepherds. However, all but one head depicted in the frescoes, that of a shepherd, had been removed in the 1628 renovation.
Badia Fiorentina