The use of microwaves is explored in an effort to further improve the recently developed lignin isolation protocol termed EMAL (enzymatic mild acidolysis lignin). Because the presence of the lignin-carbohydrate linkages seems to be rather pronounced within wood, a microwave reactor was used to replace traditional refluxing during the mild acidolysis step. This was done in an attempt to augment the selectivity of this step toward cleaving lignin-carbohydrate bonds as well as reducing the overall intensity of this step toward inducing changes in the lignin structure, thus affording lignin in greater yields and purities. Consequently, in this study the yields, purities, and structures of lignins isolated from spruce (softwood) by the EMAL protocol under various microwave conditions were examined. The variables studied included microwave power, microwave heating time, hydrochloric acid concentration and water content of the reaction medium. Microwave heating afforded EMAL samples of high purity (90%, comparable to the conventional protocol) but in significantly greater gravimetric yields. Quantitative (31)P NMR and SEC data confirmed that the structure of lignin was similar to that obtained by traditional EMALs, with comparable contents of beta-aryl ether bonds, phenolic hydroxyls (condensed and uncondensed), and carboxylic acids.