This study aimed to identify the efficiency of mechanical flower thinning (MFT) and its influence on apple fruit quality. In the first experiment, ‘Arisoo’ apple flowers were subjected to MFT with one hundred sixty-two (half) and three hundred twenty-four (full) strings at the same rotor (300 rpm) and tractor (6 km/h) speeds. Hand thinning was performed as a control. The number of removed flowers in each terminal and lateral flower cluster was slightly higher in MFT with full-strings than that of MFT with half-strings. The fruit set rate was lower in MFT with full-strings than that of MFT with half-strings. However, the use of full-strings during mechanical thinning increased the leaf damage rate compared to half-strings. Except a* value, MFT with full-strings improved flesh firmness, soluble solids content (SSC) and titratable acidity (TA), and reduced starch pattern index of fruits at harvest compared to the control. In the second experiment, ‘Fuji’ apple flowers were subjected to chemical thinning, MFT (300 rpm, 6 km/h), and MFT + chemical thinning treatments and compared with hand thinning (control). The thinning efficiency of MFT was similar to that of chemical thinning and MFT + chemical thinning treatments in terms of the removal of flowers and fruit set rates. Compared to the control, MFT, chemical thinning, and their combined treatments improved flesh firmness and SSC of fruits at harvest. TA was highest in the chemical thinning treatment compared to other thinning treatments. However, fruit size, weight, and a* value were unaffected by any treatment. In conclusion, the use of full-strings during MFT achieved optimal results in ‘Arisoo’ apples. In ‘Fuji’ apples, MFT treatment alone achieved effective results and the addition of chemical thinning after MFT had no supportive role in thinning efficiency and fruit quality.