In 1643, in Ilyinsk, by the order of Patriarch Joseph, a new wooden church was built with two altars dedicated to Saint Apostle and Evangelist John the Theologian and Saint Prophet Elijah. The construction was overseen by Archimandrite Dionysius of the Yuriev Arkhangelsk Monastery. Patriarch Joseph donated icons, books, bells, and other church property to the new temple.

Patriarch Joseph was enthroned on March 27, 1642. His ministry was marked by strict adherence to church regulations. Upon taking office, he addressed the clergy and laity with a teaching consisting of three parts, directed at bishops, the tsar, and boyars, as well as ordinary clergy. In 1643, Patriarch Joseph defended Orthodoxy in a discussion with Lutheran pastor Filgober, who arrived in Moscow with Danish Prince Waldemar. During his tenure, 36 books were published, 14 of which had not been previously published in Russia. The relics of St. Cyril of Novozeretsky, St. Savva of Storozhevsky, and Prince George Vsevolodovich were discovered. With the patriarch's funds, a silver reliquary for the relics of Prince George was made in the Assumption Cathedral of Vladimir. In 1647, a miraculous icon of the Myrrh-bearing Women was revealed in Tsarevo-Kokshaysk, and a church was built at that site. On April 5, 1652, the relics of Patriarch Job were transferred to Moscow. Patriarch Joseph paid great attention to spiritual education, and in 1649, a spiritual school was opened in Moscow at the Andreev Monastery. At the Zemsky Sobor of 1651, dedicated to the issue of the reunification of Ukraine with Russia, he proved himself to be a true patriot, firmly supporting the reunification. Patriarch Joseph passed away on April 15, 1652, mourned by the tsar, his entourage, and the people. He was buried in the Assumption Cathedral next to the tomb of the first Patriarch of Moscow, Job, at a place he chose himself before his death.

In 1643, the church clergy consisted of priest Savely Semyonov, deacon Abram Vasilyev, and sexton Stenka Pimenov. In 1669, the records noted: "In the village of Ilyinsk, the church of Saint Apostle and Evangelist John the Theologian and Saint Prophet Elijah, in the yard of priest Savva with children Senka, Oleshka, Savka, from 48 peasant households and 4 households of landless peasants."

The church housed an ancient gospel printed in 1677, with the inscription: "In honor and praise of the God-renowned temple of His and His saints, the Holy Glorious Apostle and Evangelist John the Theologian and the Holy Prophet, the fiery charioteer Elijah, in the patriarchal estate in the village of Ilyinsk, by the efforts of the sinful elder Macarius of the Chudov Monastery for eternal remembrance, and whoever detaches, sells, or pledges this book from the holy God's church and considers our promise as nothing, may God judge him with me at His second terrible coming, wanting to repay everyone according to their deeds."

After the abolition of the patriarchate, the village came under the jurisdiction of the Synodal office.

In 1792, parishioners built a stone church at their own expense to replace the old wooden one, preserving the dedication to the previous saints. A stone bell tower and fence were erected by the church. In 1868, a new carved gilded iconostasis was installed in the main church, and the walls were adorned with sacred paintings. In 1873, a new iconostasis was also placed in the Ilyinsk chapel, which was gilded in 1876.