Background: Motor and non-motor symptoms affect the life of those living with Parkinson's disease, and it is clear that exercise offers benefits in these aspects. However, the effects of adapted functional training interventions and the Mat Pilates as a form of rehabilitation for the disease in question have not yet been established. Thus, this study aims to propose an adapted functional training protocol and Mat Pilates for individuals with Parkinson's disease and to evaluate the effects on motor symptoms (balance, cardiorespiratory fitness, lower and upper limb strength, flexibility and agility), as well as , in non-motor symptoms (cognition, depressive symptoms, mood state, anxiety and finitude) by means of a randomized controlled trial. Methods: Protocol for a randomized clinical trial in which 45 individuals with Parkinson's disease will be recruited and randomly allocated to one of three groups: (1) functional training; (2) Mat Pilates; (3) control group. Both intervention groups will have 60-minute classes twice a week for 12 weeks. The primary outcome will be analyzed by balancing with the Mini-BESTest test. Secondary outcomes will include cognition, aging perspective, mood, anxiety, depression, mobility, muscle strength, handgrip strength, flexibility, range of motion, and cardiorespiratory fitness. The evaluations will be performed in the pre-intervention period (baseline), after 12 weeks of intervention, after 3 months, 6 months and 1 year of intervention. Discussion: This will be the first randomized trial to compare the effects of functional training and Mat Pilates in a population with Parkinson's disease. It is hypothesized that improvements in motor and non-motor symptoms will be greater and more lasting after functional training and Mat Pilates interventions than those that maintain their routine activities, given the benefits of exercise and the unprecedented protocols in this disease.Trial registrationRegistry name: Registro Brasileiro de Ensaios Clínicos (ReBEC)Registration number: RBR-6ckggnDate of registration: September 29, 2020. Trial was prospectively registered