Staphylococcus aureus (S. aureus) is a major global health concern and is classified by the World Health Organization (WHO) as a high-priority pathogen due to its multidrug-resistant (MDR) profile and virulence. Biofilm formation is a critical resistance mechanism, enhancing bacterial tolerance to antimicrobials up to 1000-fold. Consequently, the development of anti-biofilm therapies represents an urgent need, providing an alternative to conventional bactericidal antibiotics. Natural compounds, owing to their diverse modes of action and low resistance potential, have emerged as promising candidates. This study evaluates the antibacterial and antibiofilm activities of baicalin, quercetin, and 18β-glycyrrhetinic acid—individually and in combination—against methicillin-resistant S. aureus (MRSA) isolates. A panel of community-associated MRSA (CA-MRSA) isolates was subjected to microbiological assays, assessing effects on bacterial growth, biofilm inhibition, and biofilm eradication. Combination studies were further performed; including sequential models with thymoquinone and ciprofloxacin to assess synergistic effects. None of the tested compounds exhibited strong bactericidal activity against planktonic MRSA cells. However, baicalin and quercetin showed notable biofilm inhibition, whereas 18β- glycyrrhetinic acid demonstrated minimal effect. Quercetin exhibited a potent and dose-dependent antibiofilm activity. Combination assays revealed that quercetin–baicalin and quercetin–18β-glycyrrhetinic acid pairings produced additive inhibitory effects across MRSA strains. In contrast, the quercetin–thymoquinone combination displayed antagonistic behavior, possibly due to overlapping mechanisms of action. None of the tested compounds significantly eradicated pre-formed biofilms. The sequential treatment of an inhibitor followed by an eradicating agent has shown significant biofilm reduction in comparison to that of each compound solely. These findings demonstrate that natural compounds, particularly quercetin-based combinations, can effectively inhibit MRSA biofilm formation through non-bactericidal mechanisms. Such approaches may reduce selective pressure for resistance and offer complementary strategies to existing antibiotics. Future research should focus on elucidating molecular mechanisms of action and improving compound bioavailability and delivery to advance the translational potential of natural anti-biofilm therapies.