The effect of natural and lactic acid bacteria (LAB) fermentation processes on metabolite changes in pastes of soybeans and soybean-maize blends was studied. Pastes composed of 100% soybeans, 90% soybeans and 10% maize, and 75% soybeans and 25% maize were naturally fermented (NFP), and were fermented by lactic acid bacteria (LFP). LAB fermentation processes were facilitated through back-slopping using a traditional fermented gruel, thobwa as an inoculum. Naturally fermented pastes were designated 100S, 90S, and 75S, while LFP were designated 100SBS, 90SBS, and 75SBS. All samples, except 75SBS, showed highest increase in soluble protein content at 48 h and this was highest in 100S (49%) followed by 90SBS (15%), while increases in 100SBS, 90S, and 75S were about 12%. Significant (P < 0.05) increases in total amino acids throughout fermentation were attributed to cysteine in 100S and 90S; and methionine in 100S and 90SBS. A 3.2% increase in sum of total amino acids was observed in 75SBS at 72 h, while decreases up to 7.4% in 100SBS at 48 and 72 h, 6.8% in 100S at 48 h and 4.7% in 75S at 72 h were observed. Increases in free amino acids throughout fermentation were observed in glutamate (NFP and 75SBS), GABA and alanine (LFP). Lactic acid was 2.5- to 3.5-fold higher in LFP than in NFP, and other organic acids detected were acetate and succinate. Maltose levels were the highest among the reducing sugars and were two to four times higher in LFP than in NFP at the beginning of the fermentation, but at 72 h, only fructose levels were significantly (P < 0.05) higher in LFP than in NFP. Enzyme activities were higher in LFP at 0 h, but at 72 h, the enzyme activities were higher in NFP. Both fermentation processes improved nutritional quality through increased protein and amino acid solubility and degradation of phytic acid (85% in NFP and 49% in LFP by 72 h).