In January 1571, Skuratov led a punitive expedition against Novgorod, killing thousands of its citizens on suspicion of treason. In 1571, Skuratov was put in charge of the investigation into the causes of the Russian army's defeat by the army of the Crimean Khan Devlet I Giray. Malyuta Skuratov was killed during the siege of Weissenstein (now Paide, Estonia) in the Livonian War in 1573. He lies buried near the grave of his father in the Joseph-Volokolamsk Monastery.