The dehydration process is the basis to obtain high quality saffron and to preserve it for a long time. This process modifies saffron’s main metabolites that define its quality, and are responsible for the characteristic color, taste, and aroma of the spice. In this work, the effect of microwave dehydration on saffron main metabolites (picrocrocin, safranal and crocetin esters) from Crocus sativus L. stigmas at three determinate powers and different time lapses was evaluated. The results showed that this dehydration process obtained similar or lower crocetin esters content, and after three months of storage, higher concentration was shown in treatments at 440 W for 36 s, 55 s, and 73 s; at 616 W for 90 s; and at 800 W for 20 s. Picrocrocin content was lower and safranal content was higher in all treatments compared to the control both before and after storage. Regarding to commercial quality, microwave dehydration obtained Category I of saffron according to International Standard Organization (ISO) 3632. After three months of storage, treatments at 616 W for 83 s and 800 W for 60 s obtained lower categories. The results obtained suggest that microwave dehydration is a suitable process for obtaining high quality saffron, 800 W with 6 lapses of 20 s being the best conditions studied.