In January 1592, he was the Councilor of Ministry of Personnel (이조참의). When King Seonjo took refuge in Pyongan Province, he attempted to follow him. But he was late and he was already out of office and had no duty. He tried to defend Kaesong with his younger brother, Yi Jeong-hyeong, but failed due to the collapse of the Imjin River defense line. In April, he entered the Hwanghae Province, became a Suppressor (초토사), recruited righteous army, and entered the Yonan Fortress with them. When Japanese Army led by Kuroda Nagamasa invaded, he defeated the Japanese enemy and firmly defended the castle. With the credit, he became an Governor of Hwanghae Province. In 1593, he served as Second Minister of Military (병조참판), governor of Jeolla Province. However, after successfully defending the Yonan fortress, Yi proposed reinforcement negotiations to Seonjo, insisting on a quick end to the war, but was impeached and lost his official post. However, he was appointed to Deputy Magistrate of Jeonju (전주부윤) in July of the same year In 1596, he became the governor of Chungcheong Province and contributed to the repression of the Yi Mong-hak’s Rebellion. However, he was dismissed under the charge of arbitrarily punishing prisoners, and in December of that year, he concurrently served as the Fourth Minister of the Office of Ministers-without-Portfolio (동지중추부사) and governor of Hwanghae Province. In 1597, when the Second Japanese Invasion broke out, he protected Suyang Fortress of Haeju as a Suppressor of Hwanghae Province. After the Japanese invasions of Korea, he resigned from his official post and spent his last years writing several works in Jeongjujeongsa Temple in Pungdeok. He died on September 10, 1600.