Archbishop Ivan Dmitrievich Kasatkin (1836–1912), later St. Nicholas of Japan, was the founder of the Japanese Orthodox Church who devoted himself to improving Japanese-Russian relations during the Meiji period.

Depictions of its exotic Byzantine architecture and the unique sound of its bell often appeared in literature and illustrations of the day.

Rebuilding the cathedral became a major task for the then-ruling bishop, Archbishop Sergius (Tikhomirov), who succeeded St. Nicholas after he died in 1912.

A significant amount of funding was raised by numerous concerts by the cathedral choir, led by Victor A. Pokrovsky.

The re-built cathedral was re-consecrated on 15 December 1929, with a shorter bell tower, a modified dome, and a less ornate interior, according to design by Okada Shinichiro.