The COVID-19 pandemic has affected the lifestyles of people of all ages, conditions and occupations. Social distance, remote working, changes in diet and a lack of physical activity have directly and indirectly affected many aspects of mental and physical health, particularly in patients with many comorbidities and non-communicable diseases (NCDs). In our paper, we analyzed COVID-19 hospitalized and non-hospitalized cases according to comorbidities to assess the average monthly percentage change (AMPC) and monthly percentage change (MPC) using open access data from the Chilean Ministry of Science, Technology, Knowledge and Innovation. As expected, the infection mainly affected patients with comorbidities, including cardiovascular risk factors. The hospitalized cases with obesity and chronic lung disease increased throughout the period of June 2020–August 2021 (AMPC = ↑20.8 and ↑19.4%, respectively, p < 0.05), as did all the non-hospitalized cases with comorbidities throughout the period (AMPC = ↑15.6 to ↑30.3 [p < 0.05]). The increases in hospitalizations and non-hospitalizations with comorbidities may be associated with physical inactivity. A healthy lifestyle with regular physical activity may have had a protective effect on the COVID-19 severity and related events in the post-pandemic period, especially for the NCD population.