The use of soya and flaxseed flours fermented with Pediococcus acidilactici for wheat sourdough bread production was investigated. The protein digestibility, biogenic amine contents of soya and flaxseed sourdoughs, texture and sensory features of bread were studied. The fermentation with P. acidilactici significantly improved soya and flaxseed protein extraction and increased protein digestibility on an average by 13.5%. The concentrations of histamine (3.8 ± 2.3 and 4.0 ± 0.2 mg/kg), tyramine (4.6 ± 0.7 and 19.3 ± 1.8 mg/kg) and putrescine (66.4 ± 1.3 and 11.3 ± 3.0 mg/kg) do not present a health risk for consumers due to their relatively low levels in fermented plant products. The flaxseed sourdoughs influenced a 17.5% higher specific volume and a 4.6% lower crumb hardness of bread than those of soya sourdoughs, and did not disimprove sensory properties of bread. However, the fermented soya additives decreased acceptability of bread because of intensive taste and odour.