Fossil fuel consumption for centuries has led to widespread deposition of coal or soot particles in agricultural soils of industrialized areas. However, little is known about the impact of fossil fuel carbon (C) contamination on soil organic C (SOC) estimates. This study investigated topsoil (0–10 cm) coal C and soot C derived from incomplete combustion of fossil fuels (S_fC) in the coal-contaminated soils (CCS) and coal-free soils (CFS) from the Jiaozuo coal-crop overlapping zone in China. We explored the impact of fossil fuel C by comparing the SOC measurements determined by dry combustion and two modified Walkley-Black (WB₁₇₅ and WB₁₃₅) methods with counterparts derived from the stable C isotope technique. The results showed that the coal C and S_fC fractions accounted for 52 ± 25% and 7 ± 4% of total organic C (TOC) in the CCS. The S_fC fraction accounted for 8 ± 2% of the TOC in the CFS. No significant difference in SOC concentration was observed between the CCS and CFS (P > 0.05). Both coal C and S_fC can be completely oxidized by the dry combustion method and highly oxidized by the WB methods (WB₁₇₅: 46–95%; WB₁₃₅: 53–100%). Using the three methods to quantify SOC produced an overestimation of 20% to 7.4-fold for the CCS. Moreover, the contribution of coal C to the SOC overestimation was significantly higher than that of S_fC (P < 0.001). For the CFS, a significant overestimation (5–15%) of SOC was also detected for the dry combustion method (P < 0.001). The results suggest that direct application of routine dry combustion and WB methods can lead to serious overestimation of SOC when ignoring fossil fuel C contamination. Interestingly, we observed a sharp decrease in SOC concentration when the coal C fraction exceeded 68%, which implies that the incorporation of crop straw into highly coal-contaminated soils can act as a C source for the atmosphere. Therefore, distinguishing fossil fuel C from SOC is crucial for accurately estimating SOC in fossil fuel-contaminated soils when dry combustion and WB methods are applied.