Background: In December 2019, 27 cases of pneumonia, of unknown cause, were identified in the province of Hubei (China). The WHO declared the situation as a Public Health Emergency of International Concern, and it was finally declared a global pandemic on March 11, 2020. The Spanish Government obliges the entire population to remain confined to their homes, with the exception of essential basic services, to stop the spread of COVID-19. Home isolation implies a notable physical deconditioning. Telerehabilitation methods have reported positive experiences, and we propose to study in affected patients of COVID-19, due to the general house confinement of the entire Spanish population. Methods: Patients will be recruited in the regions of Andalusia, Murcia, and Valencia (Spain). Patients will remain confined to their homes, and there, they will carry out their assigned exercise program, which will be controlled telematically. Evaluators will attend to carry out all measurements at the beginning, during, and end of the study, telematically controlled. The patients will be randomly divided into three groups, two of them will perform a home exercise program (breathing exercises or non-specific exercises for muscle toning) and the third group will perform sedentary activities, using mental activation techniques, and will act as a sham group. We will evaluate respiratory variables and other variables of the physical state through physical tests, effort, and perceived fatigue. The data will be statistically analyzed, and the hypotheses will be tested between the groups, using the SPSS software, v.24, considering a 95% confidence interval. Discussion: We will analyze the results, in terms of the level of fatigue and perceived exertion, physical health, and maintenance of respiratory activity of two types of exercise programs, toning and respiratory, applied in patients affected by COVID-19 during the period of home confinement. We intend to investigate a field not previously studied, such as the repercussion of carrying out a toning and respiratory exercise program in these patients, in historical circumstances that no one had previously observed in Spain, since the general population has never been forced to remain confined in their homes, due to a pandemic infection, by a coronavirus (COVID-19). Observing the effects that these two home exercise programs could produce in patients infected with COVID-19, we will try to better analyze and understand the mechanisms that are associated with the worsening of breathing in this type of patient.