The ability of rhizosphere bacteria to induce systemic resistance in plants has been widely described in the literature. Various products of rhizobacteria act as signalling molecules, developing stress-like reactions in the plant. At the same time, the accumulation of peroxidase and other reactive oxygen species in the cell plays a major role, and is one of the most important plant defence mechanisms in response to various stressors. Peroxidase is a polyfunctional enzyme involved in both the generation and the utilization of hydrogen peroxide, and its activity in cells is related to plant resistance to phytopathogens and adverse environmental conditions. We measured the levels of free and weakly bound guaiacol-dependent peroxidase in the roots and leaves of wheat plants both inoculated with Pseudomonas extremorientalis PhS1 and Aeromonas media GS4 and uninoculated, under conditions of high temperatures and low humidity, with and without the phytopathogen Bipolaris sorokiniana. Following inoculation, a 1.4–5.2-fold increase in the severity of plants affected with the phytopathogen was observed. Seed bacterization decreased the number of damaged plants both with and without the phytopathogen by 1.2–2.4 and 3.2–4.7 times, respectively. Seed bacterization increased peroxidase activity in leaves and roots with and without the phytopathogen. Correlation analysis showed a statistically significant (P < 0.05) relationship between the increased activity of peroxidase in wheat leaves and roots and the reduced number of affected plants. The strongest relationship was observed between the enzyme activity in wheat roots and a decrease in the disease severity with the phytopathogen.