The present research verified the role motivational factors play in the learning process, using an undergraduate Natural Sciences course. The overall aim was to evaluate the motivation of these students, determine if motivation varied with the number of years of university attended and identify which motivational factors influence the learning of Natural Sciences. In total, 73 students, during different course offerings from 2012 to 2017, participated in the research, which corresponded to 56.5% of the total enrollment from that time frame. A questionnaire, which was organized into two parts, was employed for data collection, and scored using the Likert scale. In the first part, the following motivational factors were assessed: intrinsic motivation, self-determination, career motivation, self-efficacy and grade motivation. In the second part, the teaching strategies and activities utilized during the course were evaluated with regards to their motivational character. It was found that a majority of students were motivated and that the level of motivation increased throughout the course, being driven by intrinsic factors, that indicated that the students were trying harder to learn scientific concepts, rather than seeking approval and rewards. Furthermore, it was found that participation in projects was the most motivational activity, followed by the academic week and internships.