An exponential increase of scientific works dealing with the use of polyphenol-rich ‘natural products’ for the synthesis of bioactive AgNPs is in progress. However, a lack of fundamental studies on phytochemical compounds involved, and their role is evident. In this work, a comprehensive study of the antifungal performances of silver nanoparticles (AgNPs) synthesized exclusively with phenolic compounds (PCs) with different structures and different antioxidant capacity is presented. The experimental hypothesis is that AgNPs@PCs produced with different PCs can exert different toxicity. In particular, di-hydroxylic and tri-hydroxylic phenolic acids (caffeic acid and gallic acid) and flavonoids (catechin and myricetin) were compared. A room temperature rapid and simple AgNPs synthesis was carefully optimized, obtaining stable and reproducible colloids. AgNPs@PCs suspensions were characterized by UV–vis spectroscopy, ς-potential, dynamic light scattering and transmission electron microscopy. AgNPs@PCs radical scavenging capacity was also assessed. Finally, the AgNPs@PCs antifungal effect was tested against Aspergillus niger, particularly on spore germination and mycelial growth. The different antifungal activity was attributed to the different PCs' ability to generate/stabilize AgNPs with different shells, residual antioxidant capacity, and capacity to interact and aggregate during their 'attack' to A. niger hyphae. This work paves the way for the rational use of PCs and PCs rich-products for AgNPs-based applications.