Growing consumer awareness of clean labels is driving demand for preservative-free products yet concerns about foodborne pathogens and microbiological safety remain significant. Plant-derived compounds with bioactive properties—phytobiotics—have emerged as promising alternatives or complements to conventional antimicrobial agents. This review discusses phytobiotics, including essential oils, polyphenols, alkaloids, and organosulfur compounds, highlighting their structural diversity and antimicrobial potential. Phytobiotics combat foodborne pathogens by disrupting cell structures, inhibiting biofilms and quorum sensing, and interfering with genetic and protein synthesis. Importantly, some phytobiotics exhibit synergistic effects when combined with antibiotics or other natural agents, enhancing overall antimicrobial efficacy. The impact of phytobiotics on the microbiota of food products and the gastrointestinal tract is also addressed, with attention to both beneficial modulation and possible unintended effects. Practical applications in food preservation and supplementation are analyzed, as well as challenges related to composition variability, stability, and interactions with food matrices. Nevertheless, modern technologies such as nanoencapsulation, complexation with polysaccharides, and advanced extraction methods are being developed to address these challenges and enhance the stability and bioavailability of phytobiotics. Continued investment in research and innovation is essential to fully harness the potential of phytobiotics in ensuring safe, natural, and sustainable food systems.