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Denture-related stomatitis (DRS) is frequent oral inflammation in complete denture wearers. This study evaluated the effect of a hygiene protocol on DRS remission, local inflammatory factors, and hemodynamic responses. Thirty-three individuals were enrolled in the study. The outcomes were measured before and after 10 days of a hygiene protocol treatment consisting of brushing the palate with a soft brush and water and denture brushing with a denture-specific brush and mild soap, as well as immersion of the denture for 20 min in a 0.25% sodium hypochlorite solution. Data were analyzed by paired Wilcoxon for biofilm removal and CFU count of microorganisms. The paired T test was used to assess salivary MUC 1, cytokines, and arterial pressure (<i>p</i> < 0.05). A significant difference was found in the DRS degree (<i>p</i> < 0.001), biofilm (<i>p</i> < 0.001), microbial load of <i>Candida</i> spp. (<i>p</i> < 0.001), Gram-negative (<i>p</i> < 0.004), <i>Staphylococcus</i> spp. (<i>p</i> < 0.001), and <i>S. mutans</i> (<i>p</i> < 0.001) of the denture, and <i>S. mutans</i> (<i>p</i> < 0.001) of the palate after use of the protocol. The salivary flow (<i>p</i> = 0.2) and pH (<i>p</i> = 0.97) did not change; there was an increase of MUC 1 (<i>p</i> = 0.049) and a decrease in IL-6 (<i>p</i> = 0.038), IL-2 (<i>p</i> = 0.04), IL-10 (<i>p</i> = 0.041), and IFNγ (<i>p</i> = 0.04). There was also a decrease in systolic (<i>p</i> = 0.012) and mean arterial pressure (<i>p</i> = 0.02). The current hygiene protocol reduced the inflammation degree of DRS and promoted an improvement of local inflammatory factors and a reduction in the systolic arterial pressure of the patients.