The last buildings of the Raifa Desert were the bell tower with the gate church in honor of the Archangel Michael and the Trinity Cathedral. The construction of the bell tower began in 1889 thanks to the funding and contract of the famous Kazan philanthropist Mikhail Timofeevich Atlashev.

According to legend, the construction of the chapel was accompanied by a special sign of God's favor: one of the monks saw a blessing hand stretching out from a bright cloud above the future chapel's site. At the same time, others heard the ringing of bells associated with the death of Philaret, presumably in 1659, who was buried in the Spaso-Preobrazhensky Monastery. To obtain a blessing for the foundation of the monastery, monk Faddey approached the Kazan bishop on behalf of the monks. Metropolitan Lavrenty of Kazan and Sviyazhsk approved this initiative and sent an experienced Kazan hieromonk, Savvatiy, to establish the holy abode. In 1662, the first wooden church in honor of St. Euphemius, Archbishop of Novgorod, was erected. At the same time, a wall with two gate churches was built, one of which, dedicated to the holy Fathers who were killed in Sinai and Raifa, gave the name to the very monastery, Raifa Desert.