It is well established that there is a national problem surrounding the equitable participation in and completion of science, technology, engineering, and mathematics (STEM) higher education programs. Persons excluded because of their ethnicity or race (PEERs) experience lower course performance, major retention, sense of belonging, and degree completion. It is unclear though how pervasive these issues are across an institution, from the individual instructor, course, and discipline perspectives. Examining over six years of institutional data from a large-enrollment, research-intensive, minority-serving university, we present an analysis of racial opportunity gaps between PEERs and non-PEERs to identify the consistency of these issues. From this analysis, we find that there is considerable variability as to whether a given course section taught by a single instructor does or does not exhibit opportunity gaps, although encouragingly we did identify exemplar instructors, course-instructor pairs, courses, and departments that consistently had no significant gaps observed. We also identified significant variation across course-instructor pairs within a department, and found that certain STEM disciplines were much more likely to have courses that exhibited opportunity gaps relative to others. Across nearly all disciplines though, it is clear that these gaps are more pervasive in the lower division curriculum. This work highlights a means to identify the extent of inequity in STEM success across a university by leveraging institutional data. These findings also lay the groundwork for future studies that will enable the intentional design of STEM education reform by leveraging beneficial practices used by instructors and departments assigning equitable grades.