Complex and overlapping clinical presentation of systemic autoimmune diseases, such as Psoriatic arthritis (PsA) and Rheumatoid arthritis (RA), creates significant difficulties in early diagnosis and management. Metabolomics, as a rapidly developing field, holds a great potential to identify the intricate metabolic disturbances related to these conditions. This may assist in the early and accurate diagnosis, and personally-tailored treatment of these conditions. The current review summarizes recent metabolomics research conducted in patients with PsA and RA and employing nuclear magnetic resonance and mass spectrometry sub-techniques. The discussed studies reveal unique metabolic patterns and pathways associated with the development of PsA and RA and represent valuable information about disease pathogenesis and potential molecular-based markers. Thus, despite the substantial advances that have already been made in the field of metabolomics in systemic autoimmune diseases, there are still many gaps. First, cohort studies with larger sample sizes are required to identify and validate more metabolic abnormalities. In addition, the findings of new candidates for biomarkers must be validated, and new biofluids must be further explored for metabolomic analysis. Filling these gaps may help researchers to develop a thorough understanding of most systemic autoimmune diseases, and innovative personalized diagnostics and therapeutic strategies can be subsequently developed.