The relics of St. Stephen were left underground, and soon a stone church was built above them, which became the northern chapel of the new Trinity temple. The chapel was consecrated in 1558 in the presence of Ivan the Terrible and Tsarina Anastasia, who donated vestments for the altar, linens for the icons, and a covering for the relics of the saint. Thanks to the efforts of Abbot Amphilochius and partly funded by him, the wall paintings and the pre-altar iconostasis in the Stephen church were restored. Since 1885, all wall paintings in the monastery were done by the Alexandrov painter Fyodor Dmitrievich Lavrovsky. Together with his sons Fyodor and Dmitry, who studied at the Moscow Stroganov School, he often visited Makhra, completing numerous paintings, and in 1906 he painted the reconstructed Stephen church and restored the icons. By the 500th anniversary of the death of St. Stephen, the Stephen church was significantly rebuilt. The consecration of the rebuilt church took place on June 5, 1906, under the guidance of Archimandrite Tobias from the Holy Trinity St. Sergius Lavra, with the participation of the Makhra builder Melchizedek and the brotherhood. The monastery was closed on January 5, 1923. In 1942, the Stephen and Trinity churches, as well as the bell tower, were dismantled, and the rubble was used to build an airfield in the village of Slobodka in the Kirzhach district. In 1995, the nuns appealed for help to the president of the Rosenergoatom concern, Erast Nikolaevich Pozdychev, who, along with his staff, worked for more than ten years on the revival of the monastery. Today, the concern is headed by his successor Sergey Alexandrovich Obozov, who continues to care for the monastery. In the summer of 1996, exploratory and archaeological work began to investigate the remains of the Stephen church. The foundation made of large boulders was found to be in good condition. On October 14, 1996, the ceremonial laying of the first stone took place, and bells were brought. For the first time in 75 years, the surroundings were filled with ringing. On October 14, 1997, a cross was raised on the church, and its consecration took place on November 25. From the monastery chronicle dated November 25, 1997: "Around ten o'clock in the morning, His Holiness Patriarch Alexy II of Moscow and all Russia arrived. With the singing of the troparion to the Holy Trinity, the Primate of the Russian Orthodox Church was led to the new church. This church, built over the discovered relics of St. Stephen of Makhra and previously considered the northern chapel of the Trinity Cathedral, was originally consecrated in 1558 in the presence of Tsar Ivan the Terrible. And now, almost 440 years later, the altar in the name of St. Stephen of Makhra was consecrated by His Holiness the Patriarch. For the first time after so many years of desolation, the Bloodless Sacrifice was offered over the burial place of the Makhra miracle worker."

On the eve of the Pentecost feast, June 16, 2000, an icon of the Holy Trinity and a basma cross were installed, crowning the three-tiered iconostasis. In 2006, a covered porch was recreated against the western wall in the form it was added in 1912. By the 600th anniversary of the repose of St. Stephen, in the summer of 2006, a reliquary with a canopy was installed over his resting place, made in the basma technique with elements of embossing and casting. The author of the work was Maxim Lavdansky. From 2007 to 2010, the church was decorated with external paintings and tiles created by artists from the "Kinovar" workshop and the sisters of the monastery.