It was not long, however, before this arrangement was abandoned by Moscow, and it solidified its control over the Metropolia of Kyiv. After the death of his co-tsar Ivan in 1696, Peter I commenced an ambitious program of expansion and development, including a reworking of the Orthodox Church's administration. He effectively eliminated the position of Patriarch, replacing it with a body known as the Most Holy Synod. Over the next few decades, he succeeded in subordinating the Orthodox Church — including the Metropolia of Kyiv — into a bureaucratic department of the Russian Empire.
The Metropolitan of Kyiv would go from leading a full Metropolia containing multiple eparchies, to being simply the bishop of the Kyiv eparchy (while still keeping the honorary title of "Metropolitan"). Over the coming years, his title would even be occasionally demoted to "Archbishop".
Ukrainians were not passive in the face of these encroachments on their ecclesiastical and political life. During the Great Northern War (1700-1721), many Ukrainians, including Het'man Ivan Mazepa, sided with the forces of King Charles XII of Sweden, hoping for renewed autonomy in a strengthened Hetmanate allied with the Swedish Empire. These hopes were dashed when the Swedes and their Ukrainian allies suffered a crushing defeat at the Battle of Poltava in 1709. In a further example of the intersection of politics and religion in this era, Mazepa, who had been renowned as a builder and restorer of Orthodox churches and was major patron of iconography, was placed under an anathema by the Russian Church after 1709, one which remains in place to this day.
By the end of the 18th century, the position of Het'man had been abolished. In the 1800s, Ukraine became a de facto colony of Moscow, and even the publication of Ukrainian language books was forbidden. Efforts to make Kyivan Orthodox practice conform to the customs of the Church of Moscow were only partially successful, since leaders of the Russian Church were commenting on what they considered to be the peculiarities of religious customs in Ukraine even as late as the 1870s.
Perhaps paradoxically, Ukrainian church leaders had an outsized influence on the Russian Church, both before and after the loss of Kyiv's autonomy. The liturgical reforms carried out under Patriarch Nikon in the 1650s and '60s were largely the work of Ukrainian monk-scholars trained at the Kyiv-Mohyla Academy. The implementation of these reforms led to a schism with the "Old Believers", and it fell to Ukrainian-born bishops, such as the Archbishop of Rostov, Dymytrii Tuptalo (1651-1709), to defend those reforms. Tuptalo, who was also a poet and composer of non-liturgical devotional songs in the Baroque style, is now venerated as St. Dymytrii of Rostov in both the Ukrainian and Russian Churches, along with St. Ioasaph of Belgorod (1705-1754) and St. John of Tobolsk (1651-1715). Leading composers of sacred music in the Empire during this era, such as Dmytro Bortniansky (1751-1825), were also of Ukrainian origin.