The First Principles of Instruction (FPI) represent ideologies found in most instructional design theories and models. Few attempts, however, have been made to empirically test the relationship of these FPI to instructional outcomes. This study addresses whether the degree to which FPI are implemented in courses makes a difference to student cognitive engagement, taking into account the mediating role of individual goals. A multilevel meditation model was tested with 1,070 undergraduate students from 29 courses in a Korean university. Findings demonstrated that the influences of course-level implementation of FPI influence cognitive engagement through individual intrinsic goal orientation. Course-level implementation of FP does not directly affect surface strategy use and self-regulated strategy use; rather, the effect of FPI appears to be mediated by intrinsic goal orientations. Course-level implementation of FPI also appears to affect deep cognitive strategy use directly as well as indirectly through intrinsic goal orientation. The present study added novel evidence linking Merrill's First Principles of Instruction to cognitive engagement.