Background: Despite the robust body of evidence for the benefits of home-based physical exercise, there is still a paucity of data on the benefits of home-based cognitive training for older adults, especially in those at increased risk of clinical-functional vulnerability. As such, the present study aims to compare the chronic effects of a telehealth-delivered physical training intervention alone or combined with a cognitive training program in older adults at increased clinical-functional vulnerability risk. Methods: A randomized clinical trial will be conducted including 62 sedentary older individuals classified as at increased risk of clinical-functional vulnerability based on their Clinical-Functional Vulnerability Index score. Participants will be randomly allocated in a 1:1 ratio to one of two groups, an intervention group including physical training combined with cognitive training, or an active control group including physical training alone. Both groups will receive home-based supervised training remotely for 12 weeks and will be assessed for the primary and secondary outcomes of the study before and after the training period. Primary outcomes include cognitive function and dynamic balance with a dual task. Secondary outcomes encompass physical, cognitive, and occupational performance, functional capacity, quality of life, and anxiety and depression symptoms, as well as hemodynamic measures. Data analysis will be performed by intention-to-treat and per protocol using mixed linear models and Bonferroni’s post hoc (α = 0.05). Discussion: Our conceptual hypothesis is that both groups will show improvements in the primary and secondary outcomes. Nevertheless, we expect physical combined with cognitive training to improve cognitive function, dual task, and occupational performance to a greater degree as compared to physical training alone. Trial registration: NCT05309278. Registered on April 4, 2022.