This study aimed to evaluate the effectiveness and safety of microbiome modulating therapies for neurological disorders, focusing on Parkinson’s disease, Alzheimer’s disease, and Multiple Sclerosis. Utilizing a randomized controlled trial design with 400 participants, the study compared treatment and control groups over a 12-month period. Key outcomes included changes in neurological function, quality of life (QoL) scores, and incidence of adverse events. Analysis revealed significant improvements in neurological function and QoL for the treatment group, with notable reductions in UPDRS, MMSE, and EDSS scores (p < 0.001) and a marked increase in QoL scores (p < 0.001).