This study evaluates the effect of trehalose addition (10 or 20%, w/w) and/or sublethal homogenization (25-150 MPa) on antioxidants content (vitamin C, total phenols, and flavonoids) and activity (measured both by ABTS-TEAC and DPPH assays), as well as on microbial counts and survival to in vitro digestion of clementine juice inoculated with Lactobacillus salivarius spp. salivarius. Particle size, vacuum impregnation parameters and anti-Helicobacter pylori effect were also measured. Incubation with the probiotic improved the antioxidant properties of the juice. Homogenization pressures below 100 MPa following incubation increased both the probiotic counts in the juice and its antioxidants bioaccessibility. Adding 10% (w/w) of trehalose to the juice was effective in preventing these bioactive compounds deterioration under adverse conditions. Once homogenized, liquids containing 10% (w/w) of trehalose became as able as those without trehalose to enter a food solid matrix. Inhibition of Helicobacter pylori growth was evident in all probiotic beverages.