One of the key bottlenecks of the economically viable production of low added value microalgal products (food supplements, feed, biofuels) is the harvesting of cells from diluted culture medium. The main goals of this work were to prepare a novel flocculation agent based on spent brewer's yeast, a brewery by-product, and to test its harvesting efficiency on freshwater Chlorella vulgaris in different environments. The yeast was first autolyzed/hydrolyzed and subsequently chemically modified with 2-chloro-N,N-diethylethylamine hydrochloride (DEAE). Second, optimal dosage of modified spent yeast (MSY) flocculant for harvesting C. vulgaris was determined in culture media of various compositions. It was found that the absence of phosphorus ions decreased (0.4 mg MSY/g biomass), while the presence of algogenic organic matter (AOM) increased (51 mg MSY/g biomass) the required dosage of flocculant as compared to complete mineral medium with phosphorus and without AOM (12 mg MSY/g biomass).