Crop thinning is an important and difficult agricultural practice. Knowing the effect of the application dose of a product is a crucial element of any thinning program. The aims of this study were to investigate the effect of different metamitron doses on Gala and Fuji apples applied at fruit king diameters of between 8 and 10 mm and to determine fluorescence inhibition at the different application rates. Trials were conducted over two seasons from 2015 to 2016 in apple orchards in Lleida (Spain). Photosynthesis inhibition caused by metamitron was also analysed and measured, using chlorophyll fluorescence and biexponential pharmacokinetic models. Under the trial conditions, the application of metamitron reduced final fruit set, number of fruits per tree and crop load depending on the application rate. A dose effect was observed in all yield parameters. Moreover, when metamitron showed high efficacy, there was an improvement in fruit weight, coloration and diameter. The estimated parameters A, α and B using a biexponential equation were related with final fruit set, however the period of inhibition has to be finished before prediction can be made of metamitron efficacy in the year. The fluorescence analysis showed a dose effect, with metamitron dose increasing inhibition. Additionally, the same result was also observed in the area under curve analysis, with metamitron dose reducing the area and inhibition increasing. In all yield parameters, the fluorescence and area under curve analyses showed differences between cultivars, with the inhibition caused by metamitron higher in Gala than in Fuji. Moreover, differences between years were observed. 2015 was warmer than 2016, and the higher temperatures increased the thinning efficacy of metamitron.