Chilling stress limits processing tomato growth and yield, leading to high losses. An approach to increase the sustainability of crop production could involve the use of beneficial microorganisms. The objectives of this research were to investigate: (i) the efficacy of Funneliformis mosseae and Paraburkholderia graminis C4D1M in avoiding processing tomato damage during severe chilling stress; (ii) the synergic effect of the two microorganisms inoculated as a consortium; (iii) if the putative microorganism effects depended on the processing tomato genotype. To achieve these objectives, two experiments were carried out. In the first experiment, a modern genotype was assessed, while three genotypes were evaluated in the second experiment. At sowing, F. mosseae was mixed with peat. Nine days after sowing, P. graminis was inoculated close to the plant’s root collar. After 40 days of seed sowing, chilling treatment was performed at 1 °C for 24 h. F. mosseae mainly reduced the cell membrane injuries in term of electrolytic leakage and efficiency of photosystem II, after the chilling stress in both experiments. Conversely, in the second experiment, the consortium improved the seedling regrowth, increasing the efficiency of photosystem II. In addition, modern genotypes inoculated with microorganisms showed a better seedling regrowth.