Identifying the mental models held by students has been widely emphasized as being a pivotal aspect of effective science education. In fact, it allows us to understand students' conceptions, detect teaching-learning difficulties and tailor instruction accordingly. Hence, in this study, the plant nutrition mental models held by upper secondary students were investigated and empirically validated with the aim of detecting the most pressing learning demands and providing instructional guidelines to improve the teaching-learning of the topic. In order to unveil students' mental models a 5-question open-ended questionnaire was administered to 122 Spanish upper secondary students. Their responses were analyzed through an innovative approach that merged phenomenography and Item Response Theory. Three distinct models emerge from the analysis investigating the sequential development of students' reasoning. The first and most basic comprises students with heterotrophic explanatory ideas based on intuitive and naïve conceptions. The intermediate model consists of participants who incorporate photosynthesis and plants' gas exchanges to their models without fully grasping some key underlying concepts probably due to previous misconception inducing instruction. The upper model encompasses the few students who have autotrophic mental models and ideas which resemble the consensus Scientific Model of Plant Nutrition. The findings also reveal that the overall conceptualization level of the participants is relatively low and that several teaching-learning difficulties are strictly linked to each of the different mental models. Finally, the learning demands of the topic are described, and the implications for the teaching-learning designs aimed at overcoming those difficulties are discussed.