Pavel Florensky spent most of his life in his own house in Sergiev Posad, which he acquired in 1915. That same year, his family moved from Tiflis to Moscow to be near him. His mother, Olga Florenskaya, sisters Raisa and Yulia, and brother Andrei settled in a five-room apartment, which became communal after the 1917 revolution and the introduction of crowding policies. The Soviet authorities allowed the Florenskys to keep two rooms, but soon the apartment elder P. A. Stroeva reported the need for further crowding. As a result, five family members had to live in one room. Since 1921, Pavel Florensky worked at Glavelectro and often stayed with his family, but due to the lack of space, he had to sleep at the homes of friends V. I. Lisev and the Efimovs. In 1933, Florensky was sent to a camp, from where he continued to write letters to his family.

In 1988, at the initiative of Maria Trubacheva and the Moscow city branch of the All-Russian Society for the Protection of Historical Monuments, the former communal apartment was included in the list of historical and cultural monuments of Moscow. Academician Dmitry Likhachev was the first to propose creating a memorial museum of Pavel Florensky in Moscow. On January 22, 1989, he appealed to the participants of the exhibition "Return of Forgotten Names," dedicated to Florensky's life, calling for the preservation of Florensky's Moscow apartment and the establishment of a museum for scientific and cultural work based on it.

In 1992, the apartment received the status of a monument subject to state protection. In 1993, Archimandrite Andronic, Florensky's grandson and director of the Center for the Study, Protection, and Restoration of his heritage, sent a request to Moscow Mayor Yuri Luzhkov to create a museum. The museum was opened on December 8, 1997, on the 60th anniversary of Florensky's death.