The pursuit of novel or modified substances based on a natural origin, like flavonoids, is essential in addressing the increasing number of diseases and bacterial resistance to antibiotics, as well as in maintaining intestinal balance and enhancing overall gut health. The primary goal of this research was to evaluate the impact of specific flavonoid compounds-chalcones, flavanones, and flavones-substituted with -Br, -Cl, -CH3, and -NO2 on both pathogenic and probiotic microorganisms. Additionally, this study aimed to understand these compounds' influence on standardized normal and pathologically altered intestinal microbiomes. 8-Bromo-6-chloroflavone 4'-O-β-D-(4″-O-methyl)-glucopyranoside and 8-bromo-6-chloroflavanone showed the most promising results as bactericidal agents. They significantly limited or inhibited the growth of pathogenic bacteria without adversely affecting the probiotic's growth. Digestion in vitro studies indicated that 6-methyl-8-nitroflavone and 8-bromo-6-chloroflavone positively modulated the gut microbiome by increasing beneficial bacteria and reducing potentially pathogenic microbes. This effect was most notable in microbiomes characteristic of older individuals and those recovering from chemotherapy or antibiotic treatments. This study underscores the therapeutic potential of flavonoid compounds, particularly those with specific halogen and nitro substitutions, in enhancing gut health.