Valorization of oilseed processing wastes is thwarted due to the presence of several antinutritional factors such as phenolics, tannins, glucosinolates, allyl isothiocyanates, and phytates; moreover, literature reporting on their simultaneous extraction and subsequent practical application is scanty. Different solvent mixtures containing acetone or methanol pure or combined with water or an acid (hydrochloric, acetic, perchloric, trichloroacetic, phosphoric) were tested for their efficiency for extraction of these antinutritive compounds from rapeseed press-cake. Acidified extraction mixtures (nonaqueous) were found to be superior to the nonacidified ones. The characteristic differences in the efficacy of these wide varieties of solvents were studied by principal component analysis, on the basis of which the mixture 0.2% perchloric acid in methanol/acetone (1:1 v/v) was deemed as "the best" for detoxification of rapeseed meal. Despite its high reductive potential, hemolytic activity of the extract from this solvent mixture clearly indicated the toxicity of the above-mentioned compounds on mammalian erythrocytes. Because of the presence of a high amount of antinutritive antioxidants, the study was further extended to examine the influence of this solvent extract on the stability of waste cooking oil-derived biodiesel. Treatment with the extract harbored significant improvement (p < 0.05) in the induction periods and pronounced reduction in microbial load of stored biodiesel investigated herein. Thus, a suitable solvent system was devised for removing the major antinutrients from rapeseed press-cake, and the solvent extract can, thereafter, be used as an effective exogenous antioxidant for biodiesel. In other words, integrated valorization of two different industrial wastes was successfully achieved.