Recent technological advancement allows the synthesis of malonic acid from the bio-fermentation routeby using cost-effective raw material like biomass, which enhances its overall production. The diluteaqueous stream of malonic acid produced from the biological route needs to be recovered. Processintensification with precise operating conditions and low toxicity such as reactive separation is appliedfor extraction of malonic acid from the dilute aqueous stream by using non-toxic natural solvents likecanola oil, sunflower oil, and soybean oil with the tributyl phosphate (TBP) extractant. An in-depthexperimental analysis is performed in the present study to evaluate extraction complexation equilibriumconstant (KE(MA)), extraction efficiency (E(MA)%), distribution coefficient (KD(MA)), and loading ratio (Z(MA)). The overall loading ratio is less than 0.5 for all solvents, which signifies the formation of 1:1complexation. KD(MA) and E(MA)% with soybean oil are in range of 0.265–0.832, and 20.683–43.850, forsunflower oil is 0.208–0.763 and 17.227–42.340, for canola oil is 0.301–0.875 and 22.878–45.106. Thebehavior of TBP-malonic acid complexation equilibrium in the reactive separation process is predicted bycomparing relative basicity model values with experimental outputs. The separation process requires acontinuous column operation, and the number of transfer stages is evaluated to be 2. Furthermore, thediffusion coefficients (D(MA)) of malonic acid to the natural, non-toxic solvents with variable TBPconcentrations are evaluated by employing various empirical correlations. The present study paves theway for future research in continuous in-situ product recovery of malonic acid produced via biologicalroute.