The objective of this study was to investigate the effects of different microwave-assisted drying methods on the physical properties, bioactive compounds and antioxidant activity of beetroots. Beetroots were subjected to high-power microwave drying followed by low-power microwave drying (HMD+LMD), high-power microwave drying (HMD), low-power microwave drying (LMD), high-power microwave drying followed by hot air drying (HMD+HAD), hot air drying followed by low-power microwave drying (HAD+LMD), high-power microwave drying followed by vacuum drying (HMD+VD), and vacuum drying followed by low-power microwave drying (VD+LMD). The drying time, moisture content, hardness, color, microstructure, betalains, ascorbic acid, total flavonoids, 2,2′-azino-bis-(3-ethylbenzоthiazoline-6-sulfonic acid) (ABTS) radical scavenging activity and ferric reducing antioxidant power (FRAP) of beetroots were analyzed. The shortest drying time (67.0 min) was observed in HMD, while VD+LMD required the longest drying time of 308.0 min. There was no significant difference in the moisture content of dried beetroots prepared by different microwave-assisted drying methods. Beetroots dried by HMD+HAD showed the highest hardness of 1332.0 g, VD+LMD led to the most desirable color with the lowest total color change. Porous structures were found in beetroots produced by HMD+LMD, HMD and LMD. Beetroots prepared by VD+LMD displayed the highest content of betacyanin, betaxanthin and total flavonoids. While beetroots dried by HMD illustrated the highest ascorbic acid content of 272.3 mg/100 g dry weight (DW). In terms of antioxidant activity, the highest FRAP value of beetroots obtained using VD+LMD was 14.95 mg trolox equivalent (TE)/g DW. Meanwhile, beetroots dried by VD+LMD exhibited the largest ABTS radical scavenging activity (16.92 mg TE/g DW). Compared to other microwave-assisted drying methods, VD+LMD is a more promising method for drying beetroots.