The formation of alpha-dicarbonyl compounds and 5-hydroxymethylfurfural during industrial processing of apple juice, orange juice, and peach puree samples was investigated in this study. Changes in the concentrations of sugars, free amino acids, alpha-dicarbonyl compounds, and 5-hydroxymethylfurfural in the samples from the critical process stages such as pasteurization, enzyme treatment, concentration, were monitored. The concentrations of sugars and free amino acids showed no statistically significant change during processing. 3-deoxyglucosone was identified as the dominant dicarbonyl compound formed during orange juice and peach puree processes, while glucosone was the main one formed in apple juice samples at all sampling points. In general, total dicarbonyl compounds significantly increased (p < 0.05) in apple juice, orange juice, and peach puree samples during processing, varied between 2.04 and 28.09 mg/L, 9.16 and 31.2 mg/L, and 8.9 and 48.31 mg/kg, respectively. The concentration of 5-hydroxymethylfurfural was found to be low in apple and orange samples and not detected in peach puree samples. The presence of molecular oxygen, the temperature and the duration of the process were determined as the remarkable processing parameters that affect the formation of alpha-dicarbonyl compounds.