Ion mobility spectrometry (IMS) coupled with mass spectrometry (MS) enables the investigation of protein folding in solution. Herein we present a proof-of-concept for obtaining structural information about the folding of a protein in dependency of the amount of an organic co-solvent in the aqueous medium by means this IMS-MS method. By analyzing the protein with native nano-electrospray ionization (ESI)-IMS-MS, the impact of acetonitrile (ACN) as a representative organic co-solvent and/or pH values on the folding of an enzyme was successfully evaluated in a fast and straightforward fashion exemplified for an ene reductase from Gluconobacter oxydans. The IMS-MS results are in agreement with the findings from the NADPH-based spectrophotometric enzyme activity tests under analogous conditions, thus also rationalizing these "wet" analytical data. For this ene reductase, a higher tolerance against ACN in the presence of a buffer was observed by both analytical methods. The results suggest that this IMS-MS methodology could be a useful complementary tool to existing methods in process optimization and fine tuning of solvent conditions for biotransformations. © 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.