The emergence of multidrug-resistant (MDR) Helicobacter pylori poses a significant global health threat, contributing to gastritis, peptic ulcer disease, and gastric cancer. With conventional antibiotics showing limited efficacy, phytochemicals are increasingly recognized as natural bioactive compounds offering antimicrobial potential with favorable safety profiles. In this study, phytochemicals from Citrus limon seeds and Delphinium denudatum roots were investigated as inhibitors of essential H. pylori enzymes. A combination of subtractive proteomics and rigorous literature mining identified three essential, non-homologous, and therapeutically relevant proteins—UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC), 4-hydroxy-tetrahydrodipicolinate synthase (DapA), and aspartate-semialdehyde dehydrogenase (Asd)—as high-priority targets for intervention. Crude plant extracts exhibited notable in vitro antibacterial activity against H. pylori. High-throughput virtual screening prioritized Limonin and Panicutine as lead phytochemicals, and subsequent pharmacokinetic and drug-likeness evaluation confirmed their oral bioavailability, non-toxicity, and compliance with standard drug-likeness criteria. Molecular dynamics (100 ns) simulations demonstrated stable ligand–protein complexes, with RMSD and RMSF analyses indicating structural stability and reduced flexibility upon binding. Hydrogen bond analysis revealed persistent interactions, while Principal Component Analysis (PCA) showed that ligand-bound complexes maintained conformational stability compared to free proteins. Importantly, MM-PBSA binding free energy calculations yielded highly favorable values, confirming strong and stable interactions between the phytochemicals and the target proteins. Collectively, these integrated in vitro and in silico findings underscore the therapeutic potential of phytochemicals as natural inhibitors of H. pylori targets. Limonin and Panicutine emerge as promising candidates against MDR H. pylori, supporting alternative treatment strategies. © King Abdulaziz City for Science and Technology 2025.