Motivation becomes a very important aspect in various activities carried out by everyone, including students while studying in college. Many works of literature and publications have revealed the relationship between motivation and learning outcomes at the school level with traditional methods and this study tries to explore the topic again by using the Guided Discovery Learning (GDL) method which is different from traditional/classical learning methods. To find out differences in achieving learning outcomes through the method are based on the level of achievement motivation of students at the college level of physical education program. This study uses a quasi-experimental method with a sample of 38 college students, and the learning process is 12 offline face-to-face meetings. The level of students’ motivation was measured using a motivational questionnaire consisting of 38 questions regarding achievement motivation, and students’ cognitive abilities were measured using three lecture material tests conducted at the beginning, middle, and end of the class term. The results of the study were processed quantitatively using statistical software to see the descriptive and inferential analysis in concluding the significance of the difference between low and high-motivated samples in their achievements in sports nutrition lectures. This study reveals a significant difference in the achievement of the sample after going through GDL learning based on the level of motivation. The results of the Student T-test and Wilcoxon’s statistical difference test on the Low-Motivated (LM) sample showed an insignificant difference on the 1–2 test, and a significant difference in the achievement of tests 2–3 and 1–3 at the level of α.05. The High-Motivated (HM) sample showed the consistency of significant changes in each test carried out (1–2, 2–3, and 1–3) at the level of α.05.