Motivation cannot be measured directly but has to be evaluated through other indirect measurements, of which questionnaires are the most common. During the work with my doctoral thesis, I needed a theoretical model that took both motivation measured with questionnaires and motivation as observed in the classroom into account. This paper presents the developed model for approaching motivation in the science classroom from multiple theoretical perspectives and allows a holistic view of motivation in complex classroom situations. The model emerged from the Hierarchical model of intrinsic and extrinsic motivation by Vallerand, and the process model of motivation by Dörnyei. Both models take aspects of motivational dynamics into account. The combined holistic model contributes to motivation research by being a tool to align motivation as measured with questionnaires with motivation as seen through students’actions in the classroom. With this paper I would like to invite discussion of possibilities and limitations with motivation research from different perspectives in science education.