Due to its polyphenol content, cocoa’s potential health effects are attracting much attention, showing, among other things, cardioprotective, anti-inflammatory, anti-obesity, and neuroprotective actions. However, there is very limited information regarding the effect of cocoa on human immunity. This study aimed to establish the relationship between cocoa consumption and health status, focusing on physical activity habits and allergy prevalence in young people. For this, a sample of 270 university students was recruited to complete a food frequency questionnaire, the International Physical Activity Questionnaire (IPAQ), and a lifestyle and health status questionnaire. The results were analysed by classifying the participants into tertiles defined according to their cocoa consumption: low (LC), moderate (MC), and high (HC) consumers. The consumption of cocoa inversely correlated with physical activity and the MC group had significantly less chronic disease frequency than the LC group. The percentage of allergic people in the MC and HC groups was lower than that in the LC group and, moreover, the cocoa intake, especially moderate consumption, was also associated with a lower presence of allergic symptoms. Thus, from these results a positive effect of cocoa intake on allergy can be suggested in the young population.