The study elucidated the effect of hot water treatment (HWT) on fungicide residue degradation in apple. Residues were measured by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) during cold storage after HWT (48, 50, 52 and 54 °C for 2, 3, 4 and 5 min) of fruits. The developed method for the mixture of six fungicides (azoxystrobin, carbendizim, dithianon, difenconazole, hexaconazole, tebuconazole) was validated for linearity, specificity, selectivity, accuracy and precision using SANTE (SANTE/2020/12682) guidelines. The results of recovery ranged from 75.18 to 119.17% with 4.19–12.72% relative standard deviation. Increasing HWT temperature and duration yielded a significant reduction in residues (90–98%) in terms of processing factor. HWT of apple at 48 °C/5 min and 50 °C/2 min yielded acceptable quality fruits along with maximum reduction in fungicide residues. Fungicide reduction followed linear relationship and first-order rates. Azoxystrobin and hexaconazole dissipated at a lower rate than dithianon, difenoconazole, carbendazim and tebuconazole.