One of the key features of the new cultural systems is the control of harmful agents with environment-friendly methods. In this study, the residue levels of chlorothalonil, iprodione, bupirimate, pirimicarb, chlorpyrifos and fenoxycarb in different peach—nectarine cultivars were investigated. It was found that, with the exception of chlorpyrifos, the residue levels of all pesticides were lower than the Maximum Residues Limits (MRLs) in all peach—nectarine cultivars used. The detected levels of chlorpyrifos were higher than the MRLs in the cultivar ‘Maria Bianca’ 7 days after application, but in cv. ‘Legory Hkcb’ dropped to very low levels 27 days after application. The degradation over time of the above pesticides in fruits was investigated in the peach cv. ‘Andross’. The detected residue levels of bupirimate, iprodione, fenoxycarb, chlorpyrifos and pirimicarb in this peach cultivar were much lower than those recommended by the European Union (MRLs) 33, 22, 22, 28, and 63 days, respectively, after application, whereas the residue levels of chlorothalonil were below the limit of detection by the analytical method used. All pesticides showed a reduction over time. When examining the levels of residues of pirimicarb and chlorpyrifos in peaches (cv. ‘Andross’) sampled from different parts of the tree canopy, no significant difference was found between samples collected from the top and the middle parts of the canopy; however, residues of pirimicarb were significantly higher in samples collected at the bottom of the canopy. Overall, the pesticide regime gave residue levels much lower than those of MRLs, in all peach—nectarine cultivars. This use of chemicals is in accordance with features of the new cultural systems to produce fruits with no or minimal pesticide residues, in contrast to the conventional system in which pesticide residues are not considered. Attention should however be paid to chlorpyrifos which should be applied at least 27 days before harvest. Factors related to the cultivars and the position of fruits in the tree canopy should be considered when sampling fruits for pesticide residues analysis.