In 1400 the church was reconsecrated, after the reconstruction within the new walls ordered by Costanza Pico (daughter of Tommasino and wife of Stefanino Stefanini of Modena), enlarged to three naves in Gothic style.

Until its demolition in 1927, the Franciscan friars distributed soup or a hot meal and bread to the poor and wayfarers, including foreigners, under that portico.

Further serious damage occurred in 1798-1799 during the French campaign in Italy, but the church managed to save itself from Napoleonic destruction (which also abolished ecclesiastical orders), as it was sold together with the Oratory of Santa Rosalia.

[3] In 1824 a monument was added dedicated to the famous Renaissance philosopher Giovanni Pico della Mirandola, who died in 1494 in Florence and buried there in the Convent of St. Mark.

In 1994 the Franciscan friars left the church for good and in January 1997 it was entrusted by the bishop of Carpi Bassano Staffieri to don Luciano Ferrari, diocesan priest and chaplain of the Santa Maria Bianca Hospital in Mirandola; as rector, he was in charge of the church until, in view of his advanced age, the newly installed Bishop Elio Tinti decided to assign it to the Missionary Servants of the Poors as of 19 October 2001.

The bell tower crashed down onto the church, almost completely destroying it, of which only the façade, the northern wall (where the Pico tombs are located) and the chapel of the military shrine in the opposite southern nave were saved.

On 22 June, about a month after the first earthquake, the fire brigade began slinging and shoring up the surviving façade and the remains of the church.

At the end of the 5.02 m wide right-hand nave, already decorated with stained glass windows, is the military shrine chapel, dedicated to the fallen of all wars, which remained almost unscathed after the 2012 earthquake.

[7][8] In the left aisle, 5.36 m wide, there was a painting of St Francis Receiving the Stigmata by Sante Peranda (recovered from the rubble of the 2012 earthquake by the fire brigade and currently transferred to Sassuolo) and a precious marble altar in the chapel of the Virgin of Reggio (Madonna della Ghiara).

The most interesting part of the church was the so-called Pantheon of the Pico family, rulers of Mirandola and Concordia, located on the northern wall of the left aisle, consisting of a series of four suspended sarcophagi.

The convent next to the church was built at the same time as the church, although its presence is only documented with certainty in 1377, when the tenants and nobles of Mirandola drew up a letter in which it is stated that the convent was built from the ancient (quod ab antiquo constructum fuit Mirandulae quoddam monasterium S. Francisci) and at that time the Friars Minor Conventual had returned.

A document from 1503 attests to the presence of a large library, with manuscripts but also printed works (the relationship between Pico della Mirandola and Aldus Manutius is well known).

Due to the Napoleonic suppression of religious orders, the convent was bought by Francesco Facci in 1811, who partially demolished it the following year.

In 1823 the convent was assigned to the reformed Friars Minor (who remained until 1867); already in 1824 the Franciscan friars partially reconstructed the book heritage (which has survived to the present day and is preserved in the historical archives of the Mirandola municipal library), following a grant of 14,000 lire from the Duke of Modena Francesco IV of Habsburg-Este for the reconstruction and purchase of the garden and the remains of the old convent; the work lasted until 1828.

The post-earthquake restoration and redevelopment project envisages bringing the Eugenio Garin municipal library and cultural centre back into the former convent, which will also be equipped with a cafeteria, a conference room, the headquarters of the 'Giovanni Pico della Mirandola' International Study Centre, a new gallery for exhibitions and temporary shows, and the municipal historical archive, while the square in front of Piazza Giuseppe Garibaldi should be pedestrianised, removing the existing car park.