In the second chapel, South., Infułacka, behind the vestibule, an altar painting with the image of St.. Nicholas the Bishop and the kneeling royal couple. In the lower left corner, the figure of the founder of the painting, Fr.. Mikołaj Kiślicki, Dean of Zamość. The image is taken from 1613 and is the work of an artist from the Lviv community. The third chapel, Relics (p.w. st. Thecla or Mary Magdalene), is separated by a wooden architectural trellis with eclectic forms, baroque-gothic, with 2 half. XIX w. In a baroque altar from the mid-17th century. a considerable number of coffin-shaped reliquaries was collected. The baroque silver reliquary of St.. Jana Kantego, patron of the Zamość Academy, with statues of angels supporting university sceptres, the work of Krakow goldsmiths with 1702. Above it, a carved reliquary with a figure of the saint, probably the work of the Lviv sculpture school with 3 quarters of the 18th century. The front of the altar, painted on wooden board, depicting Maria Magdalena in a hermitage, it is baroque from the mid-17th century. Opposite the altar there is a large light brown marble epitaph by Tomasz Oleśnicki, old man from Bełz (d. 1622), decorated with two coats of arms and ornaments, signed with the artist's monogram AF.
The fourth chapel, with a bricked up entrance arcade, rebuilt in the 18th century, houses the valuable library of the Zamość chapter, containing approx. 2 thousand. volumes, mainly old prints with beautiful bindings.
On the third pillar from the side of the nave there is a modest one, in dark brown marble, epitaph plaque by Szymon Birkowski (d. 1626), an excellent philologist, a professor of medicine and a long-time rector of the Academy, brother of the famous preacher and writer Fabian Birkowski.
Stone Music Choir from 1601 it is a large-scale sculptural work. Its structure resembles a three-span arcaded loggia on Corinthian columns, covered with bas-reliefs. Designer of this work, B. Living, Here he used original and unique in Poland construction solutions, which are an example of mannerist virtuosity. The choir's outermost arcades do not rest on columns or pillars, but they are based on the keys of the low transverse arcades. The uniqueness of this view was emphasized by the originally double-sided stone fan-shaped stairs, unfortunately replaced with a 1825 spiral cast iron steps. Choir bas-reliefs, made with a not very proficient chisel, they amaze with their ingenuity and richness of floral and figural motifs, having a decorative and symbolic meaning (birds on vines and with rings in their beak). The heads on the keys of the arcades form a mysterious ensemble based on some biblical story (crowned head on the central arcade, it is King David or Solomon). Together with the heads on the nave arcades, they constitute the mother-in-law as a whole. The organs of the Maurycy Zamoyski foundation come from 1895.
There are feretrons in the courtyard (two-sided processional images). There is a rococo feretor with 2 half. XVIII w. with a depiction of St.. Dominika kneeling in front of the Madonna and Child, in a rich woodcarving frame.
In the nave, at the west wall. next to the choir - an imposing bronze shell-shaped baptismal font, with a vase supported by angels. Sophisticated on the foot, bas-relief biblical scenes with sentences referring to the Sacrament of Baptism. It is an exquisite work of Italian or French art of foundry, the only one of its kind in Poland from the Baroque era, comes from 2 quarters of the 17th century. Next to it, there is a rococo baptismal altar from approx. 1780, about the original form, with a bas-relief baptism scene, a weak chisel by a local woodcarver.
In the first from the west. at the nave. of the Academic Chapel, a late baroque altar with 2 figures of doctors of the Church and the image of St.. Jana Kantego, patron of the Academy. Above the painting is a cartouche with the coat of arms of the Academy. On the wall named, in the corner of the chapel there is an epitaph with a bust of Dominik Convalis, Franciscan, Italian from Naples, professor of theology at the Academy and censor of the books of the academic printing house (d. 1605). Epitafium to, about the features of Krakow-Pińczów mannerism, it was forged in Zamość by a not very talented sculptor, probably Błażej Gocman.
In the second chapel of the nave,, Zwiastowania NMP, there is an excellent altar painting on this subject, with 1650, brought from Italy by Jan Zamoyski Sobiepan. This free baroque copy of the famous image from the 14th century. from the Church of Santissima Annunziata in Florence is probably the work of the Florentine painter Carlo Dolci. Data 1650 (Year S. MDCL) visible on the back of the bench. An inverted text flows from Maria's mouth: "Behold the handmaid of the Lord" ("Behold the handmaid of the Lord").
A painting of the Annunciation of the Blessed Virgin Mary from the 17th century made according to the same Florentine prototype. is located in the Poznań cathedral. In turn, the image of Zamość was copied in 1839 by Feliks Pączarski and is located in the parish church in Tarnogóra near. Krasnegostawu.
There is a double epitaph on the opposite wall of the chapel: Maryna née Obrowska Leśniewska, Starościna Racibórz (d. 1612) and her son from her first marriage, Andrzej Boremelski (d. 1610). This work, characterized by a wealth of mannerist decorative forms of the Dutch type and vivid polychrome, comes from the same workshop in Gdańsk (probably van den Blocks), what the Piaskowski epitaph.
On the third inter-nave pillar, from the side of the aisle, there is an early Baroque epitaph by Paweł Paczyński, the royal secretary (d. 1626); from the side of the nave - the epitaph of Marcin Jesiotrowski (d. 1626).