The church was founded in 1892 by Portuguese Catholic priest José de Almeida Silva. After his death in 1918, the chapel remained open for prayers, but it was closed in 1924. A new chapter in the church's history began with the arrival of Russian emigrants in São Paulo. Icons for the iconostasis were created by Mikhail Lobanov, including the image of Saint Nicholas the Wonderworker. The icons of the twelve feasts were painted by artist Nikolai Mishatkin. The altar icon was brought from China by priest Fyodor Vilkok. Two large choir icons depicting Saint Alexius, Metropolitan of Moscow, and Saint Sergius of Radonezh were created by artist Dmitry Izmailovich.

The parish was closely linked to the St. Vladimir Boarding School for Russian boys in Itu. The parish's rector, Jesuit hieromonk Ioann Stoysser, repeatedly stated in 1966 and 2004 his intention to bequeath the parish to the Moscow Patriarchate. The parish organizes children's matinees and cultural evenings. There is a library at the church with classical and children's literature, and Portuguese language courses for beginners are also held.