This scoping review aimed to identify published meta-analyses of the associations of dietary soya intakes with cardiovascular, cancer and diabetes II diseases and the best relative risk estimates. A published novel assessment process combining the well-validated Cochrane Review measures, the AMSTAR 2 checklist and a published algorithm specifically designed for conducting a scoping review of similar meta-analyses was employed. This scoping review identified and evaluated twenty-eight meta-analysis reports, published between 2000 and 2021, on the associations of soya intakes with cardiovascular, cancer and diabetes II diseases. It identified eighteen significantly negatively associated risk–disease pairs for total soya intakes, four significantly negatively associated risk–disease pairs for unfermented soya intakes and four significantly negatively associated risk–disease pairs for fermented soya intakes when compared high against low intakes. The largest significant risk decrease found was gastric cancer mortalities with relative risk (RR) 0·49 (95 % CI: 0·35, 0·68); followed by colorectal cancer mortalities RR 0·59 (95 % CI: 0·41, 0·84); ovarian cancer RR 0·52 (95 % CI: 0·42, 0·66) and endocrine-related gynaecological cancer RR 0·61 (95 % CI: 0·53, 0·72). The fermented soya intake and gastric cancer risk–disease pair were identified to be significantly positively associated, RR 1·22 (95 % CI: 1·02, 1·44) when compared high against low intakes. Four significantly negatively associated risk–disease dose–responses were also identified. Being the products with lower greenhouse gas emission intensities, soya products could be the better dietary alternatives to animal products for reducing cardiovascular, cancer and diabetes II diseases and helping combat climate change.