Methods and systems for the isomerization and fermentation of xylose and hexose sugars using an immobilized enzyme system capable of sustaining two different pH microenvironments in a single vessel are disclosed. Bilayer particles are dispersed in a mixture comprising an ionic borate source and xylose. The bilayer particles have a first region with a first enzymatic activity comprising xylose isomerase and a pH of 6 or above, and a second region having a second enzymatic activity at an acidic pH.