Cyanogenic Glycosides (CG) are compounds capable of producing hydrogen cyanide. Processed pits are potential saleable by-products if CG are removed. We evaluated the effect of processing on cherry juice and its by-products by measuring CG and quality attributes. After analysis by HPLC and 1H-NMR, amygdalin was detected in kernels (13.6-23.0 mg/g), in flesh (0.07-0.09 mg/g) and in processed juice (0.06 mg/g). A significant reduction was observed in kernels after juicing (3.3 mg/g) and after 90 minutes of additional heat/acid treatment. Cherry pit oils were also extracted by expeller pressing yielding 2.9-4.4% and presenting comparable quality attributes but different aroma perception. No amygdalin was detected. After 12 weeks, sensory and quality parameters remained relatively stable. Melatonin was also determined by 1H-NMR in different matrices. Quantification was effective between 1-100 ppm for aqueous solutions and supplements. No melatonin was detected in cherry products which may be associated with the detection limit.