The development of drug-resistant bacteria as a result of the inappropriate use of antibiotics, has led to a study on other sources of drugs for the treatment of bacterial infections. Natural compounds derived from medicinal plants have long been considered a rich source of therapeutic agents. Scutellaria baicalensis has attracted attention as its root extracts are used for a variety of therapeutic purposes. Published papers involving Scutellaria baicalensis in Scopus, PubMed, and Google Scholar databases were collected and annotated for their antimicrobial and antibiofilm application. Baicalin is the most important compound derived from the roots of Scutellaria baicalensis, and it has antimicrobial, antioxidant, anticancer, and anti-inflammatory properties that can be used for the treatment of several diseases. The main active compounds were identified as natural antimicrobial and anti-biofilm agents with clear-cut mechanisms or identified molecular reports. The present review summarizes the mechanisms of biofilm formation and quorum sensing, as well as recent advances in the discovery and identification of plant-derived natural products which are antimicrobial and anti-biofilm agents. In addition, clinical trials involving plant-derived anti-biofilm therapeutics were also discussed. These newly discovered naturally occurring anti-biofilm agents are promising candidates that could provide novel strategies for combating pathogenic bacteria and treating biofilm-associated infections.