This study aimed to examine whether casein- and chicken protein-fed mice had different capacities of recovering from dextran sulfate sodium (DSS)-induced colitis. Mice were fed a chicken protein or casein diet for 14 days, which was followed by 7-day DSS treatment and then a 6-day recovery period by gavage of Akkermansia muciniphila (A. muciniphila). Compared with the chicken protein diet, the casein diet increased the relative abundance of beneficial gut bacteria, whereas DSS treatment did not induce significant differences in physiological and pathological indicators between the diet groups. During the recovery period, gavage of A. muciniphila alleviated colitis symptoms by decreasing the score of the disease activity index (DAI), spleen weight, and TNF-α mRNA level but increasing the mucus thickness and MUC2 mRNA level. Several genera, including the Ruminococcaceae NK4A214 group, Bifidobacterium, Roseburia, Ruminiclostridium and Lachnospiraceae NK4A136 group, may play a critical role. In addition, the casein diet helped DSS-treated mice recover faster from colitis, in terms of their body weight, colon length and histological score, probably due to its higher digestibility.