Isothiocyanates may have antibacterial activity against Helicobacter pylori, but there are different variables related to Brassicaceae-derived samples that could affect their efficacy. This work studied the influence of source variety, concentration, gastric digestion, and encapsulation of samples on their bioactive response against Helicobacter pylori. The antibacterial activity of raw sprouts (red cabbage and red radish) showed the highest antibacterial effect, which was consistent with a higher amount of isothiocyanates. It decreased with gastric digestion, regardless of sample encapsulation. By contrast, adult red radish leaves became antibacterial after gastric digestion. Antioxidant activity on H. pylori-infected gastric cells was similar in all samples and followed an equivalent pattern with the changes in isothiocyanates. Raw samples decreased intracellular reactive oxygen species production, but they lost this capacity after gastric digestion, regardless whether the compounds were free or encapsulated. Red cabbage sprouts, red radish sprouts, and red radish roots produced a decrease in nitric oxide production. It was consistent with a modulation of the inflammatory response and was associated to isothiocyanates concentration. Encapsulated sprout samples retained part of their anti-inflammatory activity after gastric digestion. Adult raw red radish leaves were not active, but after digestion, they became anti-inflammatory. The results obtained in this study have shown that several variables could have a significant impact on the bioactive properties of Brassicaceae-derived samples against H. pylori, providing a starting point for the design and standardization of samples with specific bioactivities (antibacterial, antioxidant, and anti-inflammatory) potentially useful for the treatment of H. pylori infection.