The aim of this study was to evaluate the effect of pesticide formulations and fruit growth stages on the Pre-harvest Interval Period (PHI). Results showed that pesticide formulations did not affect the initial deposit and dissipation rate. However, the fruit growth stage at the application time showed a significant effect on the above-mentioned parameters. Fruit diameter increases in one millimeter pesticide dissipation rates were reduced in −0.033 mg kg−1 day−1 (R2 = 0.87; p < 0.001) for grapes and −0.014 mg kg−1 day−1 (R2 = 0.85; p < 0.001) for apples. The relation between solar radiation, air humidity and temperature, and pesticide dissipation rates were dependent on fruit type. PHI could change according to the application time, because of the initial amount of pesticide deposit in the fruits and change in the dissipation rates. Because Maximum Residue Level are becoming more restrictive, it is more important to consider the fruit growth stage effects on pesticide when performing dissipation studies to define PHI.