Background: Therapeutic dietary interventions are effective treatments for rheumatoid arthritis (RA). The mechanisms to affect inflammation and clinical outcome in rheumatoid arthritis are only partly understood. Alterations in intestinal microflora are believed to be associated with disease activity in RA. Aim: To evaluate changes in short-chain fatty acid (SCFA) profiles and clinical outcome in RA during medical fasting or mediterranean diet. Methods: Fifty consecutive in-patients from an Integrative Medicine Department were included in a prospective observational, non-randomised, clinical trial. Patients underwent a 7-day fasting (MF) therapy or a Mediterranean diet (MD) as part of a multimodal therapeutic treatment approach. Results: The mean Disease Activity Score (DAS-28) significantly decreased in both groups (p < 0.001) from 5.7 ± 0.9 to 4.1 ± 1.3 in the MF and from 5.4 ± 1.4 to 4.5 ± 1.3 in the MG group, with no significant difference between the groups (p = 0.115). VAS showed a consecutive decrease of pain in both study groups which was significantly higher in the fasting group on day 7 (p = 0.049). No significant differences between the study groups were found in the profile of total-fatty acids (p = 0.069), butyrate (p = 0.611) and propionate (p = 0.419). Measurement of acetate, however, showed significant differences (p = 0.044) with an increase from 17,4 ± 9.8 µmol/g to 21,4 ± 16.4 µmol/g in MF compared to a decrease from 15,2 ± 10.4 µmol/g to 13,8 ± 9.3 µmol/g in MD. There was no significant correlation between dietary induced changes of SCFA and changes of disease activity. Conclusion: Alterations in SCFA were found in terms of significant changes to increased acetate levels in the fasting group. A correlation between changes of SCFA from intestinal microflora and disease activity in RA could not be revealed. Further studies are needed in the field of dietary inducible changes of the intestinal microflora in patients with RA.