In 1439, by the order of Novgorod Archbishop Euthymius II, a stone bell tower was built on the previous site, on the fortress wall. Some researchers, such as K. K. Romanova and D. A. Petrov, suggested that the bell tower was restored in 1455 when Bishop Euthymius established a stone bell tower at St. Sophia. However, archaeological excavations in 1995 using dendrochronology confirmed the date of 1439, determining that the beams under the foundation of the bell tower date back to 1437. There was an opinion that before the fall into the Volkhov, the bell tower was located on the city wall and was intended for small bells, and in 1455 it stood at the southwest corner of St. Sophia Cathedral, as seen in the image of Novgorod Kremlin on the Mikhailov Icon from the late 17th century. Architect Dmitry Petrov suggested that the decorative elements on the walls of the Sophia bell tower, such as niches and Gothic belts, could have been created by Western European masters involved in construction in Novgorod and the Bishop's Palace in 1433.

In the 1530s-1540s, with the reconstruction of the wall and the development of bell-casting technologies, which led to the appearance of larger bells, the bell tower was reconstructed. This period also saw the construction of a single-story annex on the side of the detinets. During the reconstruction, the number of spans increased to five, instead of the previous three, and the number of columns grew from four to six. The bell tower was crowned with five octagonal brick tents, and the height of the ringing tier was also increased. Research by Yu. E. Krushelnitsky conducted in the 1940s suggested the presence of three vaulted chambers between the bell tower and the wall originally, but according to D. A. Petrov, they were built at the end of the 15th century during the construction of new fortress walls. The appearance of the bell tower before the reconstruction by Euthymius II can be judged by images on the omophorion of Patriarch Nikon, where it is depicted with three spans, and the view of the five-span bell tower after the reconstruction can be seen in the icon 'Vision of the Bell Ringer Tarasiy.'