The paper presents the use of computed tomography examinations to assess the effect of the pitting process on the structure of cherry fruit. The Digital Volume Correlation (DTC) method was used to assess fruit pitting. The aim of this article is to evaluate internal changes in fruit volume, measure deformation, changes in weight, and changes in cherry volume as a result of pitting with various tools. For pitting there are using conventional cross tool head and innovative pitting technology using a rotary knife and a three and four-needle head. The modern VG Studio computer program, designed for tomographic reconstructions, was used for the qualitative analysis of pitting in cherry fruit. The use of modern tools for the analysis of tomographic reconstructions facilitates a range of procedures, including qualitative analysis, measurements, porosity analysis, division into materials, determination of the share of individual materials. Additionally, as evidenced in the present study, digital volume correlation is a valuable tool. Tomographic reconstructions allowed for non-destructive measurements of deformations and damage to the fruit during the pitting process. The voxel displacement tracking method was used to determine the deformations of cherry fruit caused by different pitting technologies. The research results are presented in graphical form, including histograms that taking into account the changes in mass and volume deformations. Furthermore, an analysis of fruit mass losses was performed in order to validate the DVC method. The relative change in fruit volume and mass caused by the pitting process was assessed. The research results indicate that the innovative pitting method with three-needle head is characterized by less deformation and damage to the fruit and a smaller loss of the pericarp volume. The study points that three-needle and four-needle tools result in a reduced degree of fruit degradation in comparison to cross-shaped tools. However, when assessing the exterior surface, it should be noted that additional cutting of the fruit facilitates the removal of the pit and reduces damage to the fruit during the process.