The content of harmful materials was investigated for coffee beans sold in Daejeon. Total 79 samples were analysed and 213 residual pesticides and 2 heavy metals were analysed simultaneously by GC-MS/MS, GC-NPD, GC-ECD, LC-MS/MS and ICP-MS. The instrumental method was validated with limit of detection (LOD), limit of quantification (LOQ), the linearity of standard curves. LOD of the residual pesticides was between 0.0003 to 0.0021 mg/kg, LOQ of the residual pesticides was between 0.0008 to 0.0064 mg/kg. LOD of the heavy metals was between 0.0077 to 0.0079 μg/kg, LOQ of the heavy metals was between 0.0233 to 0.0239 μg/kg. The linearity correlation coefficient for the calibration curve was between 0.9929 to 0.9999 and the recovery rate was between 95.4% to 106.1%. According to the monitoring of residual pesticides and heavy metals, no pesticide was detected in all coffee bean samples. 88.6% (70 samples) of analysed total 79 coffee beans contained at least 1 heavy metal but there was no sample which exceeded the maximum residual limit. Risk assessment was also carried out based on the content of heavy metals detected in coffee beans. The carcinogenic risk assessment to heavy metals showed that all cancer-risk (CR) values were below 10–6 and it meant that the CR due to heavy metals intake was evaluated as safe. The non-carcinogenic risk assessment to heavy metals showed that all hazard index (HI) were below 1, which was considered acceptable at the current level of exposure. The %PTWI values of lead and cadmium for 55 roasted coffee bean samples were 0.09% and 0.04% respectively, compared with the reference values. This results indicate that there is almost no health risk from heavy metal intake through the consumption of coffee beans in circulation in Daejeon.