Gastrodia elata Blume – an important medicinal crop widely cultivated and used in Asian countries especially China, when favorably dried can give high recovery/yield of its bioactive compounds. Traditionally, gastrodia tubers are processed (cured) before drying to increase their bioactive phytochemical constituents, most importantly gastrodin. Since, the conventional method is tedious and time-consuming, the current work investigates a rapid single step post-harvest curing-drying method based on microwave to achieve high yields of gastrodin from gastrodia. HPLC analysis depict that microwave drying (MWD) increased the total phenolic content by 3.4 times compared with conventional techniques. Drying kinetics depicted that MWD dehydrated gastrodia in 2 h compared with 48−59 h by conventional processes. Minimum change in surface color (ΔE: 5.8 ± 0.02) and highly porous internal structure was observed in MWD samples compared with conventionally dried samples. Low power microwave energy (100 W) yielded more phytochemical content than higher powers. UPLC/Q-TOF MS analysis of MWD gastrodia identified gastrodin and 14 other compounds. According to Spin-spin relaxation times (T₂) by LF-NMR, only bound water was present in fully dried samples, whereas all 3 water states were found in fresh and half-dried samples. Scanning electron micrographs (SEM) showed honey-comb internal microstructure of MWD samples with distinct vascular tissues. 3-dimensional volume datasets (3D X-ray) depicted porosity and pore space arrangements inside samples before and after MWD. MWD also affected the intrinsic starch and enzymes in gastrodia causing variations to phytochemicals. FTIR spectra of starches from dried gastrodia tubers indicated changes in ordered crystallinity indicating partial gelatinization during drying. Moreover, MWD also inactivated enzymes (β-D-glucosidase) that hydrolyze gastrodin to p-hydroxybenzyl alcohol, thus preventing its hydrolysis. Therefore, it was observed that MWD is a simple, rapid, economical and benign alternative technique to dry gastrodia than other conventional methods.