The COVID-19 pandemic continues to be a global health crisis. The gut microbiome critically affects the immune system and some respiratory infections are associated with changes in the gut microbiome, here we evaluated the role of nutritional and lifestyle habits that modulate gut microbiota on COVID-19 outcomes in a longitudinal cohort study that included 200 consecutive patients infected with COVID-19. Of these, 122 cases were mild and 78 were moderate, according to WHO classification. After detailed explanation by a consultant in clinical nutrition, participants responded to a written questionnaire on daily sugar, probiotic and prebiotic intake in food, sleeping hours, exercise duration, and antibiotic prescription, during the past one year before infection. daily consumption of prebiotic-containing foods, less sugar, regular exercise, adequate sleep, and fewer antibiotic prescriptions, led to a milder disease and rapid virus clearance. Additionally, data on these factors were compiled into a single score, the ESSAP score (Exercise, Sugar consumption, Sleeping hours, Antibiotics taken, and Probiotics and Prebiotics administration; 0–11 points), median ESSAP score was 5 for both mild and moderate cases; however, the range was 4–8 in mild cases but 1–6 in moderate (p = 0.001, OR:4.2, 95%CI:1.9-9.1), our results showed a negative correlation between regular consumption of yogurt containing probiotics and disease severity (p = 0.007, OR:1.6, 95%CI:1.1-2.1). Mild COVID-19 disease was associated with 10-20 minutes of daily exercise (p = 0.016), sleeping at least 8 hours daily prescribed antibiotics less than 5 times per year (p = 0.077), ate plenty of prebiotic-containing food.