Antimicrobial filtration materials based on essential oil components (EOCs) immobilized onto silicon oxide particles have been found effective for nonthermal stabilization of liquid foods (i.e., beer, juice, wine, and etc.). However, their antimicrobial efficiency depends on the food matrix. The present work aimed to assess the effect of the major constituents of liquid food matrices on the antimicrobial activity of vanillin immobilized onto silica microparticles. Silicon oxide particles were functionalized with vanillin and characterized. The maximum tolerated concentrations of different food major constituents (i.e., proteins, lipids, carbohydrates, organic acids, alcohols and minerals) were determined against Escherichia coli K12. The results showed that organic acid and alcohol had synergetic effects on vanillin-functionalized particles, and the addition of proteins, lipids or some carbohydrates inhibited their antimicrobial activity. No effects on microbial counts were found for mineral salts. The dual combinations between the synergistic and nonsynergistic food constituents showed improved antimicrobial activity compared to single compounds. The data confirmed previous in vitro experiments and could be used to predict the antimicrobial activity of the filtration system when treating real liquid food matrices.