The effectiveness of microwave-assisted sodium hydroxide pretreatments to enhance the saccharification performance of pineapple waste was evaluated. Microwave alkali pretreatments for short exposure times (up to 60 s) significantly improved the yield of the enzymatic hydrolysis compared with non-pretreated waste. The greatest increase of fermentable (35.7%) and total sugars (33.5%) was obtained at 6.375 W/g for 5 s. However, longer exposure times resulted in sugar degradation and released fermentation inhibitors, such as phenols or hydroxymethylfurfural (HMF), as a consequence of thermal degradation. Nevertheless, the obtained phenols values were not sufficient to inhibit subsequent fermentation. Scanning electron microscope (SEM) images confirmed that applying microwaves for short exposure times promoted structural changes that improved enzymatic hydrolysis. By contrast, an increase in the severity of the treatment led to a compacted structure, which hindered access to enzymes and consequently reduced the release of sugars into the medium.