Introduction: The fragmentary and whole substitution of wheat flour with flour blends is an alternative approach for producing cheaper, nutrient-rich, and comparatively advantageous gluten-free foods through fermentation. Methods: Dry samples of sweet potato, pigeon pea, and maize botanicals were purchased from local vendors, and authenticated and processed before spontaneous fermentation at room temperature. The pH and microbiological patterns of the fermenting botanicals were evaluated every 12 hours for 72 hours, using standard test protocols. Results: It revealed that the rates of growth of isolated microorganisms were affected by pH; all the botanicals fermented had a reduction in their pH values. Acids were produced during fermentation, leading to a reduction in pH. Bacteria growth on the fermenting samples on nutrient agar reveals that the bacterial load increased with fermentation time, from 7.52 Log10 CFU/g to 10.6 Log10 CFU/g (sweet potato); 6.3 Log10 CFU/g to 10.54 Log10 CFU/g (pigeon pea), and 6.3 Log10 CFU/g to 10.54 Log10 CFU/g (maize). On MacConkey agar, the bacterial load on all samples started after 24 hours of fermentation, peaked at 48 hours, and reduced gradually towards 72 hours of fermentation. There was increase in fungal growth with time from 0 to 36 hours across all samples. The microorganisms isolated can be categorized into lactic acid bacteria, spore formers, Enterobacteriaceae, Staphylococcace, yeast, and moulds. Conclusion: Fermentation of botanicals over 72 hours results in organic acid formation, which lowers pH; this attribute helps in checkmating undesirable microorganisms capable of affecting the production of gluten-free flours with good keeping qualities.