Endogenous carbon dots (CDs) in thermally processed foods have been found to possess complex physicochemical properties that may introduce uncertain effects in terms of food safety. To investigate the structure and properties of food matrix-derived CDs during thermal processing, two common roasted foods (roasted sweet potato and instant coffee powder) were used as carbon sources and their CDs were isolated and purified. The two types of CDs were then characterized using transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), UV absorption spectroscopy, fluorescence spectroscopy, and Fourier-transform infrared (FT-IR) spectroscopy. The average particle size of the sweet potato carbon dots (SP-CDs) was 3.61 nm, exceeding that of the instant coffee powder carbon dots (CF-CDs; 2.49 nm). Both types of CDs exhibited blue fluorescence when irradiated at 365 nm. FT-IR spectroscopy analysis revealed that both SP-CDs and CF-CDs possessed abundant surface functional groups, predominantly hydroxyl, carboxyl, and amino moieties. These functional groups can bind to flavor compounds and may also interact with hazardous agents such as acrylamide, raising safety concerns regarding the consumption of thermally processed foods. Nitrogen doping during thermal processing was confirmed by XPS, with the atomic percentage of carbon elements in the SP-CDs (59.93%) being marginally higher than that in the CF-CDs (58.48%). This study demonstrates that CDs derived from different thermally processed foods exhibit distinct properties, thus providing a theoretical basis for further safety assessments of endogenous CDs in food systems.