Introduction: Post-harvest fungal decay poses a major challenge to the berry industry, with Botrytis cinerea (gray mold) and Penicillium expansum (blue mold) being the primary pathogens that reduce fruit shelf life and marketability. The present study evaluates the effectiveness of chitosan- and alginate-based gel coatings, enriched with natural antimicrobial agents, in reducing fungal decay and maintaining quality in strawberries and blueberries. Methods: Chitosan (1–2%) and sodium alginate (1–2%) solutions were prepared, adjusted to optimal pH, and applied as coatings to freshly harvested fruits. Control samples were treated with water. All fruits were stored at 4 °C and 20 °C, and fungal decay, fruit firmness, and moisture loss were monitored over a 14-day storage period. Results: The results demonstrated that chitosan-based coatings significantly suppressed the growth of B. cinerea in strawberries, while alginate gels showed greater efficacy against P. expansum in blueberries, reducing decay incidence by 35–40%. Both coatings also reduced water loss and preserved fruit firmness compared to controls. Notably, the shelf life of treated fruits was extended by 4–5 days under both storage conditions. Conclusion: Chitosan- and alginate-based gel coatings represent a promising, eco-friendly alternative to synthetic fungicides for managing post-harvest fungal decay in berries. By forming protective barriers and incorporating natural antimicrobials, these coatings not only suppress pathogen development but also maintain fruit quality and reduce food waste. Further research focusing on formulation optimization, synergistic combinations of bioactive compounds, and large-scale application is recommended to facilitate their commercial adoption.