PurposeThe study was aimed to explore the potential impact of microwave heating (450 W for 2, 4, 6 and 8 min) on antioxidant activity, anti-nutritional factors, volatile and phenolic compounds of the plum kernels.Design/methodology/approachPlum kernels are rich in proteins, lipids and bioactive compounds that are mostly underused and undervalued.FindingsThe results showed that microwave heating at 450 W for 6 min significantly (p < 0.05) increased the antioxidant activity, total phenolic and flavonoid content, while the longer treatment time (450 W for 8 min) adversely affected the phenolic compounds. Most importantly, the anti-nutritional factors like amygdalin, hydrocyanic acid, phytic acid and tannin content were reduced up to 87.1, 84.7, 20.9 and 46.2%, respectively at 450 W for 6 min treatment conditions, which was confirmed from the larger shifts observed in FT-IR spectra near 1,157 cm−1. Microwave heating at 450 W for 6 min also proved beneficial in improving the bioavailability of volatile and phenolic compounds including chlorogenic acid, gallic acid, syringic acid, (+)-catechin, caffeic acid, ß-carotene, trans-ferulic acid, rutin trihydrate, 3,4-dihydroxybenzoic acid, tannic acid and quercetin by liberating them from the plant matrix.Originality/valueThe results thus indicate that controlled microwave heating could be an effective approach for the reduction of anti-nutritional factors besides leading to an overall improvement in antioxidant potential and volatile and phenolic compounds. This novel technological approach can proliferate the use of plum kernels in different diversified food formulations.