This review describes the enhanced classification of polyphenols into flavonoids, lignans, phenolic acids, stilbenes, and tannins. Its focus is the natural sources of polyphenols and an in-depth discussion of their antibacterial, antifungal, and antiviral activity. Besides a broad literature overview, this paper contains authors' experimental data according to some daily consumed vegetables such as tomatoes, different varieties of onion, garlic, parsley, and cayenne pepper and the probable relation of these activities to polyphenols. The isolation of polyphenols via conventional and ultrasonic, pressurized liquids and pulse-field extractions, as well as their methods for detection and determination, are interpreted as well. The main mechanisms by which polyphenols inhibit the growth of bacteria, fungi, and viruses, such as protein synthesis, cell membrane destabilization, and ROS production induction, are in focus. Data on polyphenol concentrations and their respective MIC or the inhibition zone diameters of different bacterial and fungal species and suppressing viral replication are depicted. The toxicity of polyphenols in vitro, ex vivo, and in vivo towards microorganisms and human/animal cells, and the safety of the polyphenols applied in clinical and industrial applications are expanded. This review also characterizes the antimicrobial effects of some chemically synthesized polyphenol derivatives. Biotechnological advances are also reported, especially the entrapment of polyphenols in biocompatible nanoparticles to enhance their bioavailability and efficacy. Polyphenols are promising for exploring molecules' novel antimicrobial substances and paving the path for effective novel antimicrobial agents' discovery, taking into consideration their positives and negatives.