In 1546 Zhu Wan was assigned as the
grand coordinator of southern Jiangxi (), a post roughly equivalent to a provincial governor and above commissioners of the military, provincial, and surveillance hierarchies. However, he was soon transferred to the coastal province of
Zhejiang the next year, as it was undergoing a military emergency in the form of the
wokou pirates. After several years of debate over the disturbances on the coast, the Ming court under
Senior Grand Secretary Xia Yan decided to appoint a new grand coordinator to manage coastal defense in the two provinces most affected by the turbulence, Zhejiang and
Fujian. In 1547, Zhu Wan was made the Grand Coordinator of Zhejiang and Concurrent Superintendent of Military Affairs for Zhejiang and Fujian Coastal Defense (), a new position specifically created to deal with the resurgent wokou problem. It was the first time in many decades that Zhejiang had a single administrative head instead of having three provincial heads. The situation on the coast had become very dire at the start of Zhu Wan's tenure as grand coordinator. In December 1547, the Portuguese had plundered
Zhangzhou, and in February the next year the cities of Ningbo and
Taizhou were struck by an unprecedented 1,000 raiders aboard a hundred ships. This raid happened whilst Zhu Wan was inspecting in Fujian, and the government troops could not stop the raiders from killing, looting, and burning government offices and homes. Despite the dismal state of coastal defence and the widespread collusion between the gentry and the pirates, Zhu Wan carried out his task energetically. He strictly enforced the maritime prohibitions, forbidding anyone from venturing out to sea on penalty of death, and put all ships to use for defence of the coast. He also publicized the names of the influential persons involved in the illegal trade, to the annoyance of the local gentry. However, Zhu Wan was not entirely against foreign trade as he accommodated an official
Japanese trading mission led by
Sakugen Shūryō in early 1548—he had no problem with foreign trade in principle as long as it was done through the proper channels. On 15 April 1548, Zhu Wan's fleet in
Wenzhou set sail for the
pirate haven Shuangyu under the command of
Lu Tang and Ke Qiao (). The fleet descended onto Shuangyu one night in June, under the cover of thick weather. Fifty-five to a few hundred smugglers perished in the attack, but leading figures such as Li Guangtou () and
Wang Zhi were able to escape. Lu Tang then razed the town and rendered the harbour permanently unusable by filling it in with stones under Zhu Wan's orders. Zhu Wan and his generals were greatly rewarded in silver for the victory, but he also drew the ire of his political enemies among the gentry, whose profits were directly affected by the destruction of Shuangyu. Eventually a pretense was found to demote Zhu Wan to the temporary position of inspector general (), the argument being one man cannot control two provinces at the same time. ==Downfall and death==