The negative impact of a sedentary lifestyle and poor diet on health is evident across the lifespan, but particularly during the university period. Usually, the diet of university students is rich in sweetened drinks and processed foods and low in fruits, vegetables and legumes. Although there is an association between maintaining a healthy diet and the frequency of cooking at home, the time currently spent on cooking or learning how to cook is decreasing globally. The main aim of this study was to explore university students’ perceptions about healthy cooking and barriers to eating healthily. A group of 26 students participated in four focus groups. Content analysis was conducted using Atlas.ti v.8. Students perceived cooking healthily as a more complicated and time-consuming process than cooking in general. Individual and environmental factors were the most reported barriers. Costs and time, among others, were the main barriers pointed out by students with regard to healthy eating. This study highlights the need to develop interventions that modify these false perceptions about cooking healthily, and to train students so that they are able to cook healthy meals in a quick, easy, and cost-effective way. Further, specific actions are required in the university setting to minimize access to unhealthy options and to promote those linked to healthy eating.