Over time, the church suffered serious damage, so that in 1677, Prince
Antonie Ruset ordered repairs and improvements; this is attested by chroniclers
Nicolae Costin,
Ion Neculce, Alexandru Amiras and Nicolae Mustea. However, not all the work was completed, and it was only in 1680, under
George Ducas, that the interior painting was finished. Many historians believe that Ruset added the large foyer, particularly as he prepared his own grave there. A minority believe it is older, likely from the time of
Alexandru Lăpușneanu. As no documents mention the structure until 1786, another hypothesis suggests a date from the later part of the 18th century. This was the position taken by the historians' committee that opted for demolition in 1890. The church was hit by fire in 1725, 1753, 1784, 1822, 1827 and 1853, and by an earthquake in 1814, as well as being affected by normal wear and tear. In 1703–1705, it was repaired by Ana, the wife of Prince
Mihai Racoviță; Prince
Ioan Teodor Callimachi undertook repairs in 1758 and
Scarlat Callimachi during his 1812-1819 reign. A document of March 1677 indicates that Antonie Ruset had decided, together with Metropolitan
Dosoftei, to turn the church into a second seat for the
Moldavia Metropolis, alongside that in
Suceava. So it remained until another metropolitan see was built in 1695. While the chronicles indicate Ruset prepared his grave here, he died poor in Constantinople, and Prince
Constantin Cantemir was placed in his crypt for a time. Others were subsequently buried there, very likely members of the princely families; several graves were removed from the
narthex during the 1884 restoration. The church was the scene of welcoming ceremonies for princes who entered Iași in order to take up the throne, and many of them were anointed there during a ceremony described by
Dimitrie Cantemir. The great religious feasts of the year were also celebrated in the church for the benefit of the royal court. The final anointment was that of
Grigore Alexandru Ghica, in October 1849. The church is associated with the activity of Dosoftei, who ran a printing press there. One of the works he put out was a renowned
Lives of the Saints from 1681 to 1686. However, after Dosoftei was taken to Poland, the printing press petered out and the next one was not set up until the time of
Iacov Putneanul, in the middle of the following century. Moreover, it functioned in a different location, the courtyard of the
current cathedral. The school from the Saint Nicholas Church, begun by
Constantine Mavrocordatos and by Metropolitan Nechifor, was reorganized by Iacov, eventually becoming among Moldavia's most renowned. It lasted until the early 19th century as among the few institutions where Romanian was the language of instruction; pupils were taught writing, reading, grammar and liturgical music. The church was endowed with books, vestments and furniture that gradually disappeared. For example, when
John III Sobieski took Dosoftei with him to Poland in 1686, he brought all the church's precious objects and clothing. Donors would constantly replenish the collection, which was fairly complete according to an 1803 inventory. When it was restored, all the church's remaining objects were divided among the city's other churches. This is how two 18th-century bells, repaired in 1817, ended up first in the cathedral yard and then behind
Trei Ierarhi Monastery. It appears that when Sultan
Mehmed IV spent a week in Iași in July 1672 while on the way to Poland, the church was used as a mosque and then remained closed until Ruset's renovation. Unusually, from the late 18th century, the church had three altars (some sources speak of two chapels), where the liturgy was officiated in three languages (Romanian, Greek and Slavonic). By the time the restoration was agreed upon, it had five dedications: Saints Nicholas, Barbara, Stephen, Mina and Catherine. ==Restoration==