The evaluation of probiotics’ efficacy in treating irritable bowel syndrome is supported by an increasing number of clinical studies based on a heterogeneous approach of products tested and the patient cohort involved. Although the role of gut microbiota dysbiosis in IBS pathogenesis and the beneficial contribution of probiotics were demonstrated, a tool to discriminate symptom-specific strains and a personalised medicine protocol are still lacking. Thus, this study employs, for the first time, a method that combines the preferred reporting items for systematic reviews and meta-analysis and multi-criteria decision analysis methods in a structured decision-making tool to analyze the efficacy of probiotic mix, in order to identify the most effective formulation and to discriminate which probiotics are more efficient in treating different symptoms. The PRISMA methodology resulted in a qualitative and quantitative analysis of 104 clinical studies from 2011 to 2021, revealing a prevalence of Lactobacillus rhamnosus, Lactobacillus acidophilus, and Bifidobacterium animalis subsp. lactis. MCDA analysis showed that formulations based on Lactobacillus rhamnosus and Lactobacillus acidophilus have the highest efficacy, especially on quality of life, bloating, and abdominal pain. This methodological approach could become more specific by modelling clinical studies according to the age and gender of patients and probiotic strain.