Agroindustrial wastes contain macronutrients and micronutrients essential for the reproduction of lactic acid bacteria. In this research, the reproduction of Weissella cibaria was experimentally optimized in a supplemented fermentation substrate (SFS) formulated from pineapple and sacha inchi wastes. Response surface methodology was used to evaluate the influence of the following independent variables: temperature (32–40 °C), pH (5.0–6.0), and stirring speed (SS) (100–150 rpm) on the following dependent variables: viability (Log10 CFU mL−1), biomass production (BWc), lactic acid production (LA), biomass yield (YBwc/S), biomass volumetric productivity (VPWc), LA volumetric productivity (VPLA), carbon source consumption (CSC), N2 consumption (N2C), and specific growth rate (µ). The experimental optimization of multiple responses presented a desirability of 76.8%, thus defining the independent variables of the process: temperature = 35.1 °C, pH = 5.0, and SS = 139.3 rpm; and the dependent variables: viability = 10.01 Log10 CFU mL−1, BWc = 2.9 g L−1, LA = 19.4 g mL−1, YBwc/S = 43.9 g biomass/g CSC, VPWc = 0.49 g L−1 h − 1, VPLA = 3.2 g L−1 h−1, CSC = 17.2%, N2C = 63.6% and µ = 0.28 h−1. From these, viability, YBwc/S, CSC, N2C, and LA presented significant statistical differences, while the independent variable with the least important effect on the process was pH. Under optimal conditions of temperature, pH and SS; SFS favors the reproduction and viability of W. cibaria. This provides evidence of a sustainable alternative for the production of probiotics in the context of circular economy.