Schoell received the 1995 AAPG Best Paper Award and was recognized by the American Association of Petroleum Geologists as authoring one of the top twenty most notable geology-related papers of the 1980s. Specifically, the AAPG recognized Schoell for his paper "Genetic Characterization of Natural Gasses" which describes how the correlation between C concentration, the variation of carbon and hydrogen isotopes in methane, and carbon isotope variation in ethane can be used to qualitatively characterize the composition of natural gasses.
In 2008, Schoell received the annual Alfred Treibs Award. This award is given on a yearly basis by the Geochemical Society in recognition of scientists whose research has made significant contributions to the understanding of geochemical processes. Schoell received this honour in response to his work with stable isotope analyses which revolutionized fossil fuel research and greenhouse gas tracing.