We aimed to analyse the impact of COVID-19 during 2020 and 2021 on the prescription of enteral nutritional support and its expenditure in the Community of Madrid, Spain, compared to pre-pandemic data from 2016 in the general population vs. elderly. We analysed official electronic prescriptions of all public hospitals of the Community of Madrid. The population over 75 years of age have the higher prescription of nutritional supplements (p < 0.001 vs. other age groups), with no differences between the 45–64 age group compared to the 65–74 age group (χ2 = 3.259, p = 0.196). The first wave of COVID-19 or the first time there was a real awareness of the virus in Spain is similar in a way to the first peak of prescription of enteral nutrition in March 2020. The second peak of prescription was observed in the over 75 age group in July 2020, being more pronounced in December 2020 and March–April of the following year (F = 7.863, p = 0.041). The last peaks correspond to summer 2021 and autumn of the same year (p = 0.031—year 2021 vs. 2020, p = 0.011—year 2021 vs. 2019), where a relationship between increased prescription of enteral nutrition and COVID-19 cases is observed. High-protein and high-calorie dietary therapies were the most prescribed in patients with or without diabetes. All of this entailed higher cost for the Community of Madrid. In conclusion, COVID-19 significantly affected the prescription of nutritional support, especially in the population over 75 years of age.