Non-centrifugal cane sugar (NCS) is characterized by its content of carbohydrates, phenolic compounds, antioxidants, and minerals responsible for its functional properties. A few of these properties change during NCS production owing to thermal processing. This is particularly true when physical and chemical changes occur. This study investigated the effects of three concentration technologies (calandria (CAL), marmite (MAR), and refractance window (RW)) on food safety, functionality, and physical properties. The acrylamide content, antioxidant capacity, phenolic, sugar, and mineral content, color, moisture, glass temperature, and microstructure were determined. The results showed that most of the parameter changes were related to the temperature degradation processes, showing an inverse relationship with phenolic content and a direct relationship with acrylamide content. Sugar content (sucrose inversion and reactive fructose) is related to the Maillard reactions that occur during thermal processing. Caramel colorations were observed with high phenolic content (14.20–18.70 mg/kg) and low acrylamide contents (up to 40 μg/kg). The best results were obtained with concentration technology that employed lower temperatures (marmite). These results suggest that the new concentration technologies used in this study could be an alternative to the traditional process, allowing better quality, functional, and safe food products.