Inflammation is a major cause of chronic diseases. Several studies have investigated the effects of soy intake on inflammatory biomarkers; however, the results are equivocal. The aim of this study was to conduct a systematic review and meta-analysis of clinical trials that evaluated the effect of soy consumption on inflammatory biomarkers. Medline, Scopus, ISI Web of Science, and Google Scholar were systematically searched, up to and including May 2020, for clinical trials that evaluated the effects of soy and soy products on tumor necrosis factor α (TNF-α), Interleukin-6 (IL-6), Interleukin-2 (IL-2), Interleukin1-β (IL1-β), and Interferon gamma (IFN-γ) in adults. A random-effects method was used to calculate overall effects, and subgroup analyses were performed to discern probable sources of inter-study heterogeneity. A total of 28 clinical trials were included. Although soy consumption reduced TNF-α (Hedges’ g= −0.28; 95%CI: −0.49, −0.07), it had no significant effect on IL-6 (Hedges’ g= 0.07, 95% CI: −0.14, 0.28), IL-2 (MD= −1.38 pg/ml; 95%CI: −3.07, 0.31), IL1-β (MD= −0.02 pg/ml; 95%CI: −0.08, 0.03), and IFN-γ (MD= 1685.82 pg/ml; 95%CI: −1604.86, 4976.50). Subgroup analysis illustrated a reduction in TNF-α in in parallel designed studies, at dosages ≥100 mg of isoflavones, and in unhealthy subjects. The present study showed that high doses of isoflavones in unhealthy subjects may yield beneficial effects on TNF-α.