Investigations that focused on the protective role of probiotics against Surgical Site Infections (SSI) in multiple-trauma (MT) patients are generally few, probably due to the complexity of the concept of trauma. We aimed to assess the efficacy of a four-probiotic regime to reduce the incidence of SSI in MT patients, with a brain injury included. MT patients, being intubated and expected to require mechanical ventilation for >10 days, were randomly allocated into placebo (n = 50) or probiotic treatment (n = 53) comprising Lactobacillus acidophilus LA-5 (1.75 × 109 cfu), Lactiplantibacillus plantarum UBLP-40 (0.5 × 109 cfu), Bifidobacterium animalis subsp. lactis BB-12 (1.75 × 109 cfu), and Saccharomyces boulardii Unique-28 (1.5 × 109 cfu) in sachets. All patients received two sachets of placebo or probiotics twice/day for 15 days and were followed-up for 30 days. The operations were classified as neurosurgical, thoracostomies, laparotomies, orthopedics, and others; then, the SSI and the isolated pathogen were registered. A total of 23 (46.0%) and 13 (24.5%) infectious insults in 89 (50 placebo patients) and 88 (53 probiotics-treated) operations (p = 0.022) were recorded, the majority of them relating to osteosynthesis—17 and 8, respectively. The most commonly identified pathogens were Staphylococcus aureus and Acinetobacter baumannii. Our results support published evidence that the prophylactic administration of probiotics in MT patients exerts a positive effect on the incidence of SSI.