Thinning is essential and important for the quality of peach and nectarine crops because of its impact on fruit size and next season’s flower bud initiation, but hand-thinning is a costly practice and an unacceptable alternative. Researchers have been trying to introduce new thinners for almost thirty years, replacing hand-thinning. In this study, the quantitative and qualitative effects of some compounds used as thinning agents were examined on the ‘Alberta’ peaches and the ‘Sun King’ nectarines. This study has been carried out in a commercial orchard in Semirom, Isfahan, Iran during 2015–2016. Treatments included lime-sulfur (6%, 8% and double application of 6%), 10 mL L−1 fish oil, ammonium thiosulfate (20, 25 mL L−1 and double application of 20 mL L−1 ), the plant growth regulator Apogee (300, 450 mg L−1 and double application of 300 mg L−1 ), hand-thinning of flowers (at full bloom) and hand-thinning of fruits (at pit hardening). The temperature at the application time of treatments on peach and nectarine trees was above 15°C and the sky was sunny. Results showed that all of the treatments, except for 300 and 450 mg L−1 Apogee significantly thinned the fruit to 61%. The treatments increased fruit weight (42%), volume (46%), total soluble solids (TSS) (28%), TSS/titratable acidity (TA) ratio (47%) and color (37%) as compared to control. However, there were no significant differences in TA of fruits among the samples. In terms of yield, various treatments differed significantly. The highest yield for Alberta peach was achieved by the control (123 kg/tree) and the lowest yield was obtained for the single application of 20 mL L−1 ammonium thiosulfate (85.41 kg/ tree). In ‘Alberta’ peaches, the biggest fruit (125 cm3 ) was observed with the double application of 20 mL L−1 ammonium thiosulfate and fruit-thinning by 114 cm3 . Double application of these chemicals often resulted in more blossom thinning than a single application. The blossoms and fruits were hand-thinn