The name of this place is likely connected to the word "alder": a stream called Olkhovets flowed here, and Olkhovskaya Street has also been preserved. In 1687, a wooden church was mentioned at this site, and in 1714, a stone church was built with funds from Peter I and Tsarevna Praskovya Ivanovna, daughter of Ivan V. Construction was delayed due to a ban on stone work throughout Russia, except for St. Petersburg. The building was later reconstructed.

It was here in 1799 that A.S. Pushkin was baptized.

In the first quarter of the 19th century, the upper tiers of the bell tower were rebuilt. In 1837, the main part of the church was completely dismantled, and the construction of a new majestic building began, designed by architect E.D. Tyurin, which was completed in 1845. The enormous church still towers over Yelokhovskaya Square today. The bell tower, adorned with columns at the corners of its tiers, is one of the tallest in Moscow.

In 1889, the refectory was raised by architect P.P. Zykov. After the revolution and the closure of the Kremlin churches, the Cathedral of Christ the Savior, and the Church of the Epiphany in Dorogomilovo, the Yelokhovsky church was granted the status of a cathedral, and nearby was the office of Metropolitan Sergius (Stragorodsky). Attempts to close the Epiphany Cathedral were made, but none were successful. After the war, it officially became the Patriarchal Cathedral and the see of the Patriarchs of Moscow and All Russia, a status that lasted until 1991.

All central services of the Russian Orthodox Church and its most significant events during the Soviet era took place here. In 1943 and 1990, the enthronement of new Patriarchs of Moscow and All Russia occurred in the cathedral. Two of them were buried here: Patriarch Sergius in 1944 and Patriarch Alexy II in 2008. Their tombs are located in the northern and southern chapels, respectively.

In 1991, the status of the Patriarchal Cathedral was transferred to the Kremlin's Assumption Cathedral, after which the Epiphany Yelokhovsky Cathedral became a cathedral.