Surface pitting is a serious postharvest physiological disorder in sweet cherries that is observed as skin depressions developed days after bruising. This work aims to compare two cultivars displaying different pitting susceptibilities (‘Kordia’: relatively resistant; ‘Sweetheart’: relatively susceptible) using metabolomics profiling and cell wall sugar characterization at different developmental stages and during postharvest storage. Kordia was significantly firmer than Sweetheart, with 1.4-fold more alcohol-insoluble residues (AIRs). A significant correlation was observed between AIRs and deformation, indicating that the highest yields of cell wall material are positively correlated with the resistance to rupture. Additionally, free D-galacturonic acid was higher in pitted Sweetheart samples, likely indicating greater pectin degradation in this susceptible cultivar. Higher contents of the p-coumaric acid derivatives L-5-oxoproline and D-galactose in Sweetheart cherries were found. The metabolic changes during storage and cell wall composition could influence the susceptibility to surface pitting.