The church of S. Nicola is documented in 1097, described as depending from the Monastery of S. Michele at the Verruca. Scholarly tradition, perhaps not groundless, holds that it was founded by Marquis Ugo di Tuscia at the end of the 10th century, in an area with many buildings already belonging to the Tuscia family.

The lower part of the facade is decorated in the style typical of Buscheto (11th century): its dead arches on pilasters framing the doors with alternating rhombs and rose windows and two-tone marble facing are a superb example of the Pisan Romanesque style. We do not know what the appearance of the second story was to be,nor the date of the brickwork, perhaps 16th century. The unusual octagonal bell tower, with an interesting cantilevered spiral staircase built between the two cylinders of the tower (which Vasari held was the inspiration for St Patrick’s well at Orvieto), was erected in the 13th century.

The property passed to Augustinian monks in 1296, who had enlarged it by 1313. Other work was carried out during the 14th century when the Church acquired the wooden Crucifix attributed to Giovanni Pisano, now in the chapel beside the main altar, and the precious Madonna and Child painted on wood, in the chapel of the Madonna delle Grazie, attributed to Francesco Traini.

The painting of St. Nicolas saving Pisa from the Plague is from the early 15th century; it is famous for being one of the oldest and most detailed representations of Pisa. Work on the eight chapels and the vaulted ceiling began in 1572; the chapel of the SS. Sacramento is by Matteo Nigetti (1614). In 1792 the parishioners of the suppressed Church of S. Lucia de’ Ricucchi came under this parish which is also the seat of the Confraternity of S. Lucia.