To analyze the gut microbiota of patients with rheumatoid arthritis (RA) according to disease activity. An observational cross-sectional study of 110 patients with RA and 110 age- and sex-matched controls was performed. Patients were classified according to the disease activity (DAS28 ≥3.2 or DAS28 <3.2). Clinical and epidemiological variables were included. The gut microbiota was analyzed using 16S rRNA sequencing and bioinformatics analysis based on QIIME and PICRUSt. A multivariate analysis was performed to identify factors associated with inflammatory activity. The mean DAS28 indicated remission/low inflammatory activity in 71 patients (64.5 %) and moderate/high activity in 39 (35.5 %) during follow-up. Alpha and beta diversity analysis revealed differences in gut microbiota between the 3 study groups. In the moderate/high activity RA, we observed a significant change in the abundance of genera compared with the other groups. The abundance of Collinsella and Bifidobacterium was increased in RA patients compared with controls. The metabolic profile of gut microbiota was characterized by differences in pathways related to Biosynthesis, Generation of Precursor Metabolites/Energy, and Degradation/Utilization/Assimilation between the 3 groups. The factors associated with cumulative inflammatory activity in RA were age (OR 95 % CI, 1.065 1.002–1.131), obesity (OR 95% CI, 3.829 1.064–8.785), HAQ score (OR 95% CI, 2.729 1.240–5.009), and expansion of the genus Collinsella (OR 95% CI, 3.000 1.754–9.940). The composition of gut microbiota differed between patients with RA and moderate/high activity, patients with remission/low activity, and controls. The genus Collinsella, age, obesity, and physical function were associated with cumulative inflammatory burden in RA. Display omitted •The intestinal microbiota is altered in patients with rheumatoid arthritis (RA), however it is important to clarify the association between gut dysbiosis and cumulative inflammatory burden in RA.•The genus Collinsella seems to play an important role in the cumulative inflammatory burden within established RA.•Likewise, other factors such as age, obesity, and physical function were associated with higher inflammatory activity in RA patients.•Therefore, future studies on the treatment of these factors for the control of cumulative inflammatory burden in RA are necessary.