Physical activity levels during the COVID-19 pandemic have been decreasing and this may be a risk factor for development of emotional eating and its associated factors. The aim of the study was to analyze the factors associated with emotional eating among individuals with different physical activity levels during the COVID-19 pandemic. Data relating to the pandemic on physical activity, emotional eating, sociodemographic data, perceptions about lifestyle habits, body satisfaction, and perceptions about eating habits and food consumption were collected. Factors associated with emotional eating in the group of active and inactive individuals were observed using multiple linear regression controlled for age, sex, BMI, and monthly income. Emotional eating for the active group was associated with perceived stress, body dissatisfaction, and increased consumption of sweets and desserts. In addition to these factors found among the active group, working or studying >8 h/day, sleep worsening, increased amount of food consumed, increased purchase of food through delivery, and increased vegetable consumption were also associated with emotional eating for the inactive group. These findings suggest a potential protective role of physical activity in the appearance of factors associated with emotional eating during the COVID-19 pandemic.