Background Multiple sclerosis (MS) is a progressive autoimmune neurodegenerative disorder characterized by inflammation, demyelination, and axonal damage. Current disease-modifying therapies demonstrate limited efficacy with substantial adverse effects. Ayurveda and yoga have demonstrated disease-modifying potential through anti-inflammatory, immunomodulatory, and neuroprotective mechanisms. Objective This study aims to evaluate the efficacy of a three-month Integrated Yoga and Ayurveda Management (IYAM) program as an adjunct to standard care in MS patients. Primary outcomes include clinical disability (EDSS), functional capacity (MSFC), quality of life (MSQOL-54), cognition (AVLT), and psychological parameters (HARS/HDRS). Secondary outcomes encompass neuroimaging (brain volume, connectivity), immune biomarkers (Th1/Th2/Th17/Treg cells, cytokines, telomere length), autonomic function (HRV), and gut microbiome composition. Methods In this assessor-blind randomized controlled superiority trial, 60 MS patients (McDonald criteria 2017, disease duration