During the Russo-Turkish War of 1788-1791, Gudovich commanded a separate corps at Hadjibei (Odessa) and Killia. Promoted to general-en-chef, Gudovich took command of the troops in the Caucasus and the Kuban Valley. He captured the fortress of Anapa on 22 June 1791, garnering the Order of St. George (2nd class) and a golden sword with diamonds. Over the next five years, he began construction of a series of fortification along the Caucasus and was awarded the Order of St. Andrew the First Called in 1793.

Disappointed with Valerian Zubov’s appointment to command troops against Persia, he resigned from his position in early 1796. However, following Paul’s accession to the throne, Gudovich was appointed to replace Zubov in the Caucasus. In 1798, Gudovich became the Governor General of Kiev and the Podolia gubernia. However, following a disagreement with the emperor, he was discharged from the army in June 1800. After six years in retirement, he was called back to service in 1806 and took command of the Russian troops in the Transcaucasia. During the Russo-Turkish War of 1806-1811, he fought at Arpachay, Akhaltsikhe, Akhalkalaki and Gumri. In 1808, Gudovich became seriously ill (lost one of his eyes) and resigned from his positions. After recuperating, he became the Governor of Moscow on 7 August 1809 but was removed from this position due to poor health in February 1812. Gudovich spent the last years of his life at his estate at Olgopol in the Podolia gubernia, where he died in January 1820.