The name of the monastery spread throughout the surrounding area, and one of the seven hills of Moscow is now known as "Ivanovskaya Gorka".

According to one version, the monastery was founded in the 14th or 15th century in Zamoskvorechye, near Pyatnitskaya Street. This is recalled by the church on Chernigovsky Lane, dedicated to the Beheading of St. John the Baptist. In the 1530s, Princess Elena Glinskaya, the mother of the future Tsar Ivan IV the Terrible, moved the monastery to its current location, across the river. At that time, a stone cathedral was built in honor of John the Baptist, a single-domed church with three altar apses and three porches. Ivan the Terrible paid special attention to the monastery, and the first tsars of the Romanov dynasty also made donations. Besides the cathedral, there was a gate church of the Origin of the Honorable Wood of the Life-Giving Cross of the Lord. However, these buildings have not survived to this day.

The Patriotic War of 1812 caused damage to the Ivanovsky Monastery: after the French left, it was recognized as devastated and closed. The cells became apartments for employees of the Synodal Printing House, and the churches became parish churches. In 1859, it was permitted to restore the monastery with funds from Colonel Elizabeth Makarova-Zubacheva. Almost all the monastery buildings, including the churches, were dismantled, and in their place, according to the project of architect M.D. Bykovsky, a new complex was built in 1860 and 1879, which has survived to this day. The new cathedral was executed in the neo-Renaissance style, with elements of Russian architecture, inspired by the church of Santa Maria del Fiore in Florence. The faceted dome of the cathedral is pierced with double windows and topped with an "onion" dome, surrounded by small pyramids with crosses. The northern entrance to the monastery is marked by two bell towers, characteristic of Catholicism, but topped with spires, which is a Russian motif. Thus, M.D. Bykovsky combined various styles in the monastery complex. The buildings of the cells with the church of Righteous Elizabeth were executed in the same spirit.

The Ivanovsky Monastery served not only as a monastic abode but also as a prison. Two of the most famous episodes are associated with women. The first was the landlady Darya Saltykova, known as "Saltychikha" for her cruelty and murders of peasants. Stripped of nobility and property, she was imprisoned in the monastery dungeon and displayed to Muscovites in a cage. The second prisoner, nun Dosifea, on the contrary, was hidden from outsiders. She was considered the secret daughter of Empress Elizabeth Petrovna and Count Alexei Razumovsky. Having lived in the monastery for almost 25 years, she was buried in 1810 in Novospassky Monastery next to the burial place of the Romanov boyars, which indirectly confirms her kinship with the imperial dynasty.

After the revolution, the monastery ceased to function as a monastery: in 1918, one of the 11 concentration camps in Moscow was opened here, later transformed into a correctional labor house. In 1924, the Moscow factory-labor colony was established under the NKVD. Later, the cathedral became an archive storage, and the cells housed the Higher Legal Correspondence School of the Ministry of Internal Affairs of the USSR. Only in 2000 were services resumed, the monastery restored its status, restoration work was carried out, the marble iconostasis of the cathedral was recreated, and frescoes were restored. A chapel in honor of John the Baptist was built from the side of Malaya Ivanovskaya Lane, where an ancient monastery icon that survived the revolution is kept. Today, the monastery is officially called the Ioanno-Predtechensky Monastery, which is more correct from a canonical point of view, but not entirely accurate historically.

The main cathedral of the monastery, the church of the Beheading of St. John the Baptist, has an unusual architecture for Orthodox churches. It was built in the 19th century based on Italian basilicas, in particular, the Florentine cathedral of Santa Maria del Fiore.