The yacon roots are rich in fructooligosaccharides (FOS) and highly perishable. Drying is crucial for food quality and extending shelf life. However, preserving thermosensitive compounds, such as FOS, poses a challenge in conventional drying methods. In this regard, microwave drying and ethanol pretreatment (ET) have emerged as promising solutions for maintaining nutrients and reducing drying time (DT). The objective of this study was to assess how ET and sample temperature affect quality and process parameters during intermittent microwave drying of yacon. Drying at 52°C treated with ethanol was the one that stood out for presenting the highest fructan retention (64.1%), low DT, lower energy consumption (EC) (364.00±5.03kWhkgwater-1), higher retention of antioxidant capacity (73.9%) and total phenolic content (77.5%), and slight variation in color parameters. Therefore, microwave drying with a controlled temperature of yacon pretreated with ethanol effectively reduces DT and EC by maintaining quality parameters.