You may face the Cleanrot Knight twice in Elden Ring, but he isn't the only challenging boss you'll encounter in that area. Caelid is home to a sizable population of Cleanrot Knights, many of whom make their homes in the Shaded Castle and the Aeonian Swamp.
Combat with the Knight is dangerous because of the Rot it spreads, but it is still worth it. The Cleanrot armor set and some powerful weapons that can be used by any build can be obtained from normal enemies, but the dungeon boss versions of these enemies drop thousands of Runes and other useful items if you defeat them.