Using the MixAlco process, biomass can be converted into carboxylic acids, which can be chemically converted into mixed alcohol fuels. This study focused on the use of countercurrent fermentation to anaerobically convert sugarcane bagasse and chicken manure to mixed carboxylic acids using a mixed culture of mesophilic microorganisms from terrestrial and marine sources. Bagasse was pretreated with lime to increase digestibility. The continuum particle distribution model (CPDM) simulated continuous fermentors based on data collected from batch experiments. This model saves considerable time in determining optimum operating conditions. For an 80% bagasse/20% chicken manure fermentation with terrestrial inoculum at a volatile solids loading rate (VSLR) of 7.36 g/(L of liquid.d) and a liquid residence time (LRT) of 8.88 d, total carboxylic acid productivity, total acid selectivity, and yield were 2.49 g/(L of liquid.d), 0.581 g of total acid/ g of VS digested, and 0.338 g of total acid/g of VS fed, respectively, at a concentration of 18.7 g of total acid/ L. At the same VSLR and LRT, fermentation with marine inoculum gave higher total acid productivity, total acid selectivity, and yield than fermentation with terrestrial inoculum. For an 80% bagasse/20% chicken manure fermentation with marine inoculum at a VSLR of 3.83 g/(L of liquid.d) and an LRT of 12.1 d, total carboxylic acid productivity, total acid selectivity, and yield were 1.38 g/(L of liquid.d), 0.667 g of total acid/g of VS digested, and 0.359 g of total acid/g of VS fed, respectively, at a concentration of 16.2 g of total acid/L.