Abstract: Background and Objective: Anti-nutritional factors such as phytate, tannin, polyphenols and trypsin inhibitors bind to nutrients and prevent their bioavailability. This study investigated the effect of alteration in the natural ecology of microorganisms by lactic acid bacteria (LAB)-consortium on the anti-nutritional factors of bambara groundnut flour during fermentation. Materials and Methods: Bambara groundnuts were processed into flour, fermented spontaneously and with LAB-consortium (Lactobacillus rhamnosus, Lactobacillus reuteri, Lactobacillus plantarum, Lactobacillus nantensis, Lactobacillus fermentum, Pediococcus acidilactici and Lactobacillus brevis) previously isolated from maize and sorghum. Results: The result showed significant (p<0.05) decrease in tannin, phytate, polyphenol and trypsin inhibitor activity with increasing fermentation period. The decreases in the anti-nutritional factors were more in the samples fermented with LAB consortium from maize and LAB consortium from sorghum than spontaneously fermented sample. Conclusion: This suggested that altering microbial ecology of bambara flour by LAB-consortia during fermentation has potential in decreasing the anti-nutritional factors and improve bioavailability of nutrients.