Residual biomass obtained after microalgae lipid extraction is rich in carbon and nutrients and has great potential for use as a substrate in anaerobic digestion, microalgae cultivation, and plant cultivation. However, residues from organic solvents can make it unfeasible to use the biomass in these applications. In this work, ethyl acetate (EA) and hexane-ethanol mixture (HE) were used to evaluate the yield and quality of lipids extracted from the microalga Scenedesmus obliquus BR003. Also, the toxicity of these solvents to anaerobic digestion, microalgae cultivation, and seed germination was evaluated at concentrations similar to those found in the residual biomass after lipid extraction. Lipid yields were 83.1% and 55.4% for HE and EA, respectively, where EA extracted mostly neutral lipids. In the HE mixture, hexane showed no significant effect in toxicity assays due to its low solubility in the aqueous fraction. However, ethanol in this mixture migrates to the aqueous phase, and the effective concentrations at 50% (EC50) were 3.78, 26.97, and 4.97 g L−1 for methanogenic archaea, S. obliquus, and lettuce seeds, respectively. The EA showed EC50 values of 18.74, 18.02, and 5.85 g L−1 for methanogenic archaea, S. obliquus, and lettuce seeds, respectively. The EA was less toxic to anaerobic microorganisms and lettuce seeds when compared to ethanol, which was less toxic to S. obliquus, making EA an environmentally friendly solvent for industrial use. Our study provides novel information on the criteria of solvent selection when aiming at resource recovery from residual microalgae biomass after lipid extraction.