Aims Ankylosing spondylitis (AS) is a widespread and chronic inflammatory autoimmune disease of unknown provenance. Naturally occurring peptides and proteins have shown significant promise as modulators of immune responses. Thus, the aims of this study were to assess the protective effects of the bioactive peptide IQW (Ile-Gln-Trp) with respect to inflammatory indicators, gut microbiota and oxidative stress, and to examine the potential mechanisms of these effects. Methods and Results A mouse model was prepared by four injections of human proteoglycan extract (2 mg) in dimethyldioctadecylammonium solution (2 mg) over an interval of 2 weeks. Enzyme-linked immunosorbent assay results for the markers of oxidative stress and inflammation in the AS mice revealed increased concentrations of malondialdehyde, IL-6, IL-1 beta and TNF-alpha, along with decreased concentrations of catalase (CAT), glutathione peroxidase (GSH-PX) and superoxide dismutase (SOD). Treatment with IQW was found to decrease the concentrations of IL-6, IL-1 beta and TNF-alpha, and increase the concentrations of CAT, GSH-PX and SOD. Moreover the quantification of the microbiota via 16s rRNA sequencing revealed a reduced microbial diversity in the AS mice, while a significantly increased microbial diversity was displayed by those treated with IQW. Whereas, there was a significant reduction in the relative abundance of Bacteroidetes and an increased relative abundance of Verrucomicrobia in AS mice, this was reversed following the IQW treatment. Conclusions The results demonstrated that IQW exerts a beneficial influence in AS by delaying progression of the disease, reducing the arthritic grade of intervertebral joints, altering the concentrations of cytokines and modulating the microbial diversity and composition. Significance and Impact of the Study Oral IQW treatment might represent a new approach to mitigate the onset and development of AS.