Heating of batch tubular reactors with fluidized sand baths and with microwaves resulted in distinctive sugar yield profiles from pretreatment and subsequent enzymatic hydrolysis of corn stover at the same time, temperature, and dilute sulfuric acid concentration combinations and hydrothermal pretreatment conditions. Microwave heated pretreatment led to faster xylan, lignin, and acetyl removal as well as earlier xylan degradation than sand baths, but maximum sugar recoveries were similar. Solid state CP/MAS NMR revealed that microwave heating was more effective in altering cellulose structural features especially in breakdown of amorphous regions of corn stover than sand bath heating. Enzymatic hydrolysis of pretreated corn stover was improved by microwave heating compared to sand bath heating. Mechanisms were proposed to explain the differences in results for the two systems and provide new insights into pretreatment that can help advance this technology. Published by Elsevier Ltd.