Inflammation is a major cause of chronic diseases. Several studies have investigated the effects of soya 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 soya 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 soya and soya products on TNF-α, IL-6, IL-2, IL-1β and interferon γ (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 twenty-eight clinical trials were included. Although soya 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 (mean difference (MD) = –1·38 pg/ml; 95 % CI –3·07, 0·31), IL-1β (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 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.