Plant extracts contain valuable sources of biologically active molecules and, lately, have attracted scientific and industrial interest as inhibitors of food-borne pathogens and growth stimulators of beneficial microbes. In this vein, the aim of this study was to explore and exploit the effect of Aloysia citrodora extracts as potent functional regulators of food microbiota by stimulating the growth of probiotic strains and by suppressing the evolution of common food-spoilage and pathogenic bacteria. Aqueous and ethanolic extracts of A. citrodora, rich in polyphenols, were prepared and their phytochemical composition was unveiled by LC-triple quadruple and LC-QToF mass spectrometry. The growth stimulatory activity of a wild-type Lacticaseibacillus rhamnosus strain, along with L. rhamnosus GG, used as a control, was assessed by monitoring cell growth in the presence of sodium chloride, bile salts, thermal stress, and alcohol. We found that the aqueous extract stimulated the growth of probiotic strains at 0.5 mg/mL. At the same concentration, stimulatory activity was observed for the wild-type L. rhamnosus in the presence of bile salts and alcohol and for L. rhamnosus GG in the presence of NaCl and under thermal stress. The ethanolic extract of A. citrodora exhibited prebiotic activity at 0.25 mg/mL, but did not promote the growth of the strains under the stress conditions tested. In addition, minimum inhibitory (MIC) and minimum bactericidal concentrations (MBC) against food-spoilage and pathogenic microbes were determined. The strongest growth inhibitory activity of foodborne pathogens was noted by the A. citrodora ethanolic extract, while the aqueous A. citrodora extract had no effect against Escherichia coli. Importantly, the spoilage and pathogenic microbes tested were more sensitive to the extracts than the probiotic strains, indicating a significant contribution to the functional regulation of food microbiota, provided that they are used at the optimum concentration.