Alternatives to improve the stability and activity of enzymes have been rising in the last years due to the potential industrial application of these catalysts. However, the enzymes characteristics in terms of stability and catalytic efficiency can reduce, in some cases, due to the reaction conditions. Due to a lack in the literature concerning structural information related to the new commercial Eversa® Transform 2.0 enzyme (NS-40116) we investigated the conformational structure by spectroscopic and mass spectrometry techniques after exposure in permanent magnetic flux density (0.7 and 1.34 T) in recirculation mode (1, 2, and 4 h) at 0.06 L·min. The influence of pH on the enzymatic solution associated with the magnetic flux (pH 5, 7, and 9) was also evaluated. Under the best reaction condition (pH 7 after 4 h in a recirculation mode at 1.34 T), enzyme activity 77% higher than the control sample was obtained. Mass spectrometry techniques showed changes in the NS-40116 tertiary structure. Thus, the application of magnetic fields as an enzymatic pre-treatment showed to be a promising technique and a viable alternative to increase the enzymatic activity since it is a low cost, environmentally friendly, and ease operation process.