Multiple-choice tests are very handy in assessing students’ conceptual learning involving various competencies. But when students got low scores in an ordinary multiple-choice test, it is not easy to identify in which items did they do the guessing, and in which concepts did they understood differently. This study aims to assess students’ conceptual understanding of lessons in plate tectonics employing a three-tier multiple-choice test. A three-tier multiple-choice test was administered to one hundred one (101) grade, ten students. The results of the said three-tier test showed that 20.40 % have scientific knowledge about the concepts presented to them, 6.24 %of the students grasped the concepts but were uncertain with their answers, 33.46% of the students have misconceptions, while 19.31% did not understand the concept and 21.12 % were just guessing. The three-tier test developed can be utilized during formative assessments to determine both the least mastered skills and specific concepts that need to be clarified. The findings of this study can help teachers and researchers to develop appropriate interventions and teaching methods that take into account the students’ alternative conceptions and promote the improvement of their conceptual understanding of a given science topic.