Following his completion of his PhD, Schoell began working for the German Geological Survey focusing on hyper saline hydrothermal vents in the Red Sea. From 1984 to 2001, Schoell worked for Chevron Oil Field Research Company in La Habra. During this time, he published his most cited paper, "Biogenic methane formation in marine and freshwater environments: CO reduction vs. acetate fermentation—Isotope evidence". In this paper, Schoell et al. discussed how hydrogen and carbon isotope composition analysis can be used to identify different biogenic methane production pathways from its water and CO precursors.  This paper went on to win the 1995 AAPG Best Paper Award.  In addition to this, while working for Chevron in 1984 Schoell requested funding from Chevron to fund John Hayes of Indiana University to develop continuous-flow compound-specific isotope analysis. This development allowed Schoell to make a variety of discoveries including the ability of steranes and hopanes in the Lacustrine Green River Formation could be used as a proxy for water paleo-depths.
During his time with Chevron, Schoell introduced Mudgas isotope analysis to Chevron and the natural gas industry, and worked in a variety of international locations including locations throughout the Americas, Southeast Asia and Africa as well as parts of Oceania.
In 2001, Schoell went on to establish a natural gas consulting company, GasConsult International, Inc. of which he was the CEO and president of until 2015. GasConsult specializes in ZR-LNG (zero-refrigeration liquified natural gas), LH2 (liquid hydrogen) and OHL (optimized liquid hydrogen) technologies and offers clients opportunities to transition to these technologies, and is now under the direction of Bill Howe.
In 2019, Schoell founded GasXpse which applies geochemical fundamentals to provide natural gas related consulting services and provide scientific advising for natural gas-related subjects. Further, Schoell has co-authored 76 publications in the field of geochemistry.