Santiago has garnered some accolades for his research and teaching endeavors. He received the Faculty Award for Teaching Excellence from the School of Informatics at Indiana University in 2006. In 2013, he was inducted to the League of Educational Excellence in the University of Michigan Medical School, and was awarded the Endowment for Basic Science Teaching Award from the same institution. He was also Visiting Professor of Excellence, Department of Chemistry, University of Barcelona, Barcelona, Spain.
Schnell was recognized with James S. McDonnell Foundation 21st Century Scientist Award in 2010. He is Fellow of the Royal Society of Chemistry, Fellow of the Royal Society of Medicine and Fellow of the Royal Society of Biology. He is a Corresponding Member of the Academia de Ciências da América Latina. Schnell is an elected Fellow of the American Association for the Advancement of Science for distinguished contributions to the field of mathematical biology, particularly for the theoretical modeling of complex biochemical reactions and optimal estimation of their rates.
In 2023, The Society for Mathematical Biology honored him with the Arthur T. Winfree Prize for his outstanding contributions to many areas of biology, and in particular his seminal work on enzyme kinetics. Schnell's theories and mathematical modelling of enzyme catalyzed reactions have been transformative for the fields of catalysis and enzyme kinetics while leading, at the same time, to a resurgence of new mathematical biology research in enzyme kinetics. The Society for Advancement of Chicanos and Native Americans in Science conferred upon him the 2023 SACNAS Distinguished Scientist Award in recognition of his significant contributions to enzyme kinetics and the creation of a fundamental quantitative enzymological model of the Polymerase Chain Reaction.