Introduction: Parkinson’s disease (PD) is the second most prevalent degenerative neurological disorder globally. Comorbid major depressive disorder (MDD) is a common occurrence which adds considerably to disease burden. This protocol presents a study designed to investigate the effect of add on probiotic supplementation on MDD in patients with PD. Methods: We designed a phase IIb, randomized, triple-blind, placebo-controlled study to evaluate the efficacy and safety of probiotics as an adjuvant treatment to selective serotonin reuptake inhibitors (SSRI) for patients with mild to moderate PD and MDD.Participants will be randomized to probiotics (n=62) or placebo (n=62) arms using a permuted block randomization approach. Co-primary outcomes include changes in Montgomery-Åsberg Depression Rating Scale (MADRS) scores and SSRI equivalent doses, which will be compared between groups using a bivariate joint model. Secondary outcomes will include changes in both Beck Depression Inventory-II (BDI-II) score and levodopa dose, which will be analyzed using t-tests or Mann-Whitney tests as appropriate. Concurrent validity between MADRS and BDI-II will be assessed using Pearson’s or Spearman’s correlation tests. Safety will be evaluated by comparing discontinuation rates and adverse events between groups using chi-square. Data will be analyzed using intention-to-treat and per-protocol analyses, and missing data will be addressed using multiple imputation methods. Discussion: Probiotics represent a potential new approach to managing depression in patients with PD by targeting the gut-brain axis. The results will offer crucial information about the safety and efficacy of a low-cost and readily available supplement that may alleviate depression in this vulnerable population.