As microscopic colitis causes chronic diarrhea due to inflammation in the colon, treatment typically involves bulk forming agents like psyllium, antimotility and antiinflammatory agents such as steroids can also be used.

Some cases of MC are caused by a side effect to certain medications so removing the offending medication can help.
Otherwise the main treatments are anti-diarrheals like imodium and a topical steroid called budesonide.