Biocides for bio-based binder compositions are disclosed. Bio-based binders include those having a nutrient source such as carbohydrate, protein or fat, which can serve as an energy source for organisms to grow in areas that contact binder. Principal areas that contact bio-based binder in a fiberglass insulation manufacturing process include the raw ingredients, the binder chemicals, the prepared binder dispersions, the forming hood and related equipment, the final insulation product and, importantly, the cleaning systems and washwater arising from cleaning the manufacturing equipment and/or forming the product. Frequently the washwater is stored until re-cycled for re-use. Storage may take place in tanks, towers, vats and even outdoor reservoirs, all of which may harbor the growth of unwanted organisms, for which a biocide is desirable.