This study aimed to mitigate the inhibitory effect of leftover organic solvent (CH3Cl, chloroform) on anaerobic digestion of lipid-extracted microalgae waste (LEMW). Food waste leachate (FWL) was added as a co-substrate and a two-stage fermentation process (H2 production with acidogenesis + methanogenesis) was adopted. The result of the first batch experiment, conducted in the absence of chloroform, showed that as the FWL addition ratio increased up to 60% on chemical oxygen demand (COD) basis, there was a gradual increase in the amount of H2 produced. At 80% addition, however, there was a huge drop in H2 yield, accompanied by a drop in pH. In the presence of chloroform (100–900 mg CH3Cl/L), the mixture (LEMW:FWL = 40:60) exhibited a much higher tolerance than that of LEMW alone, which could be ascribed to the co-metabolic degradation of chloroform by FWL addition. At 600 and 900 mg CHCl3/L, the degradation efficiency dropped below 40% for LEMW alone, while it was maintained above 90% in the mixture. A H2 yield of 36 mL H2/g COD, equivalent to 2.6% of the energy content in the feedstock, was attained from the mixture at 600 mg CHCl3/L. The H2 fermented effluent was then fed to a continuous methanogenic reactor at HRT 40 d, and 82% of energy content in the feedstock was further gained in the form of CH4. Although the energy gained from H2 production was negligible, most of the chloroform was degraded during acidogenesis, which resulted in a successful CH4 conversion.