Faculty research productivity studies typically focus on the scholarly performance of the individual researcher, although environmental and organizational conditions that are largely outside of the researcher’s control can significantly impact that performance. From an institutional effectiveness perspective, it is imperative for the higher education administrators and leaders who share the responsibility of managing and supporting their university’s research enterprise to understand how the institutional environment itself impacts the productivity of its research community. In this sequential mixed methods study, a quantitative framework was tested for assessing institutional effectiveness in research administration based on the assertion that this concept can be measured indirectly, at the departmental level, based on the calculation of a program’s residual scholarly output. This is the difference between the actual amount of scholarly output a program produces compared to the predicted amount of scholarly output that its resources suggest it is capable of producing. The assumption is that the institution’s effectiveness in supporting research is largely reflected by the extent to which a program over- or under-produces scholarship based on its level of resources. The residual scholarly output was calculated for each Ph.D.-granting biomedical engineering program in doctoral universities with a Carnegie classification of “highest research activity” for the period of 2014 through 2016. A sampling of those programs that achieved among the highest and lowest residual productivity levels then became the subject of a qualitative inquiry where researchers and administrators were interviewed with two goals in mind. The more ostensive goal was to reveal what factors, characteristics, resources, and conditions distinguish under- and over-producing programs for the purpose of informing best and worst practices in research administration. Equally important, the second goal was to determine if the quantitative framework was actually successful in distinguishing institutional effectiveness in supporting research. The study concludes that the quantitative framework proved to be a successful method for detecting institutional effectiveness in supporting research, and that the primary distinguishing characteristic between high and low-functioning environments was how well programs were able to reduce the general administrative burdens that researchers face, particularly in grant management and the operation of research laboratories.