At first glance, the interior of the church presents a plain architecture where everything seems to converge towards the high altar, between the presbytery and the choir.

The high altar stands majestically on five steps. It displays a triumphant arch supported by eight fluted columns with Corinthian capitals. In the centre of the frontispiece is a depiction of the Blessing Eternal Father, in polychrome and gilded wood, and at either side we admire the annunciation of the Angel Gabriel (left) to the Virgin Mary (right).

The altar was completed in the second half of the XVI century by the stonemasons Antonius (son of the late Cristoforo da Bisson) and Simone Sorella, on a design attributed to Girolamo Campana (1552-1626). The top part of the altar is by an unknown author. In 1649 Baldassare Longhena (1552-1626) adorned the table with fine Baroque style carved marble pieces; he also positioned, above the eight Corinthian columns, a baroque frontispiece. The statues of St. Francis and St. Anthony were placed between the altar columns (but in 1864 they were moved to the right and left of the altar).

Situated on the walls we find two sepulchral monuments, the left one dedicated to the doge Andrea Gritti, the right one to his ancestor and tutor Triadano Gritti. The two monuments of identical style have been attributed to Sansovino, Palladio and Scamozzi.

At the entrance of the presbytery, on the left side, we find an elegant gothic image of  'Madonna of Humility'  painted by an unknown artist at the end of XIV century. The board, of a particular beauty, comes from the 'Congregation of  St. Mary of Humility of the Celestial Church' .

Under the icon we find Blessed Matteo da Bascio's sepulchral tomb, he was one of the great reformers of the Franciscan Order and co-founder of the Order of the Friars Minor Capuchin. He died on the 5th of August 1552 at San Moisè and was buried first in the choir of the church and later was laid in the current location by decree of the Apostolic Nuncio Lodovico Bacatello, because the crowd of devotees was obstructing the recital of the divine office.

The choir was part of the primitive church and underwent heavy consolidation restorations in 1724 and in 1905. The stalls and cornices of the choir were made in 1710, while the backs were inlaid by Gian Marcantonio Canozio of Lendinara and belonged to the XVI century old choir.

The XVIII century old organ was built by the Franciscan Pietro Nacchini, an active builder of excellent organs in Italy and Dalmatia.

Above the choir stalls we find many paintings. On the left: a) St. Francis interceding for a sick woman (circa 1620), by Pietro Mera; b) Christ blessing Venice, by Palma the Young (post 1604); c) Immaculate by Giorgio Lazzarini (1710-1714); d) St. Peter of Alcantara giving communion to St. Theresa of Avila, by Umile of Foligno (XVII century); e) the Virgin with baby Jesus answers St. Francis and St. Domenic's prayers to free  Venice from the plague, by Domenico Tintoretto (1631).

On the right side of the choir: a) the Virgin pleads Christ to free Venice from the plague, by Domenico Tintoretto (1631); b) St. Peter of Alcantara miraculously crosses a river, by Umile of Foligno (XVII century); c) Holy Trinity, by Francesco Maggiotto (end of XVIII century); d) Dinner at the Pharisee's home, by Andrea Michieli, named Vicentino (beginning of XVII century); e) the Virgin presents the Baby to St. Francis, by Palma the Young (beginning of XVII century).