Marine biofouling presents a major challenge for the maritime industry and marine ecosystems, traditionally managed through biocide-based antifouling (AF) coatings. However, the environmental toxicity of these biocides has intensified the search for sustainable, environmentally friendly alternatives. In this study, a novel approach using flavonoid-based compounds as environmentally safe AF agents is presented. Building on the previous identification of the prenylated dihydrochalcone (DH345P), the first reported dihydrochalcone with AF activity, here a series of dihydrochalcone analogues was synthesized and evaluated to further explore the structure-activity relationship studies (SAR). Among the compounds studied, dihydrochalcone (10) emerged as the most effective, exhibiting the best performance regarding anti-settlement activity (EC50 2.34 µM), while remaining non-toxic to A. salina. To assess real-world applicability, compound 10 was incorporated into marine polyurethane (PU)-based coatings, which resulted in significantly reduced mussel larvae adherence compared to blank control coatings. These findings highlight dihydrochalcone-based compounds as a promising scaffold for sustainable AF agents. Considering their AF potential, non-toxic profile and feasible synthesis, flavonoids such as compound 10 might be explored as an alternative for conventional AF biocides, paving the way for greener marine coatings.