Retention of bioactive compounds in white- (WFP), yellow- (YFP), red- (RFP) and purple (PFP)-fleshed potatoes after drum-drying (DD) and Refractance Window™ drying (RW) was compared with freeze-drying (FD). Processing, generally, did not influence total phenolics. Total carotenoid was high in YFP, but decreased with DD. Both DD and RW decreased lutein concentration in YFP. The RFP and PFP had the highest total anthocyanin, and their concentrations were decreased by DD. RW decreased total anthocyanin in PFP only. Total antioxidant activity in WFP was higher with DD but lower with RW. In contrast, DD and RW drying had no significant effect on total antioxidants in YFP, RFP and PFP. Therefore, drying generally decreased antioxidants, with FD and RW retaining the highest concentration of bioactive compounds.