Helicobacter pylori (H. pylori) is considered the most common bacterial pathogen colonizing stomach mucosa of almost half the world’s population and is associated with various gastrointestinal diseases (from digestive problems and ulcers to gastric cancer). A lack of new drugs and a growing number of H. pylori antibiotic-resistant strains is a serious therapeutic problem.As a mixture of natural compounds, propolis has antimicrobial activity based on high concentrations of bioactive polyphenols (mainly flavonoids and phenolic acid derivates). The chemical composition of tested Georgian propolis is characterized by the presence of flavonoids aglycones, and phenolic acid monoesters, e.g., pinobanksin-5-methyl ether, pinobanksin, chrysin, pinocembrin, galangin, pinobanksin-3-O-acetate, pinostrobin and pinobanksin-3-O-butanoate, or isobutanoate and methoxycinnamic acid cinnamyl ester. The anti-H. pylori activity of 70% ethanol water extracts of 10 Georgian propolis samples was evaluated in vitro by MIC (minimal inhibitory concentration) against the reference strain (H. pylori ATCC 43504) and 10 clinical strains with different antibiotic-resistance patterns. The strongest anti-Helicobacter activity (MIC and MBC = 31.3 µg/mL) was observed for propolis from Orgora, Ota, and Vardzia and two from Khaheti. Lower levels of activity (MIC = 62.5 µg/mL) were found in propolis obtained from Qvakhreli and Pasanauri, while the lowest effect was observed for Norio and Mestia (MIC = 125.0 µg/mL). However, despite differences in MIC, all evaluated samples exhibited bactericidal activity. We selected the most active propolis samples for assessment of urease inhibition property. Enzyme activity was inhibited by propolis extracts, with IC50 ranging from 4.01 to 1484.8 µg/mL. Principal component analysis (PCA) and hierarchical fuzzy clustering (dendrograms) coupled with matrix correlation analysis exhibited that the strongest anti-Helicobacter activity was connected with black poplar origin and high flavonoid content of propolis. Samples with lower activity contained higher presence of aspen markers and/or dominance of non-flavonoid polyphenols over flavonoids. In summary, Georgian propolis can be regarded as a source bioactive compounds that can be used as adjuvant in therapy of H. pylori infection.