Kiwi and pepino fruits are most valuable fruits as they contains substantial amounts of nutrients and bioactive compounds. These fruits exhibited several health potentials such as antioxidant, antiinflammatory, antiobesity, antihyperlipidemia, and anticancer properties. However, studies on the effect of microwave and conventional drying methods on the antioxidant activity and bioactive compounds of kiwi and pepino fruits are limited. Therefore, this study was conducted to assess the effect of microwave and oven drying methods on antioxidant activity, total phenolic, and phenolic compounds of kiwi and pepino fruits. Drying of the fruit samples was carried out using conventional (70 °C for 20 h) and microwave (720 W for 3 min) ovens. 1,1-diphenyl-2-picrylhydrazyl scavenging and colorimetric Folin–Ciocalteu assays were used to assess the antioxidant activity and total phenolic contents, respectively, of fresh and dried fruits. Both drying methods significantly (p < 0.05) decreased the moisture contents of both fruits compared to untreated controls. Concomitantly, drying methods also enhanced (p < 0.05) antioxidant activity and total phenolic content of both fruits with the highest improvement being observed for microwave-dried fruits compared to untreated controls. In addition, a significant increase was observed in catechin and 1,2-dihydroxybenzene content of kiwi and pepino after drying process. However, microwave drying method reduced the amount of 3,4-dihydroxybenzoic acid in kiwi (ranging from 34.120 to 9.350 mg/100 g) and pepino (varied from 33.414 to 15.445 mg/100 g). Generally, the highest antioxidant activity and phenolic contents were reported in microwave oven dried samples, followed by samples dried in oven and fresh fruits. The results revealed that microwave drying could be more useful in fruit drying than conventional drying. In addition, dried kiwi and pepino fruits contains substantial quantities of phenolic compounds with high antioxidant activity compared to fresh fruits, and thus they are considered as healthy food.