In this study, effect of two chemical compounds (i.e., 1-octanol and hexanal) respectively from the alcohol and aldehyde groups on thermophilic (55±2 °C) anaerobic process digesting the waste produced at a paper industry was investigated. In this scope, possible inhibition was monitored by the cumulative methane (CH4) yields in the batch reactors digesting the paper waste as the feedstock at concentrations of 0.005%, 0.05%, and 0.5% for each compound. Comparing the effects of the two different groups with the control reactor having only the paper waste as the substrate, the results revealed that adding 1-octanol and hexanal up to 0.05% concentrations had some synergistic effect on biogas yield (i.e., from 3% to 12% enhancement). Accordingly, the highest methane yields were 550 and 567 mL/g-VSfed, respectively on average in the presence of 1-octanol and hexanal at a concentration of 0.05% while the cumulative methane yield was observed as 490 mL/g-VSfed for the control reactor. With the exception of 1-octanol at 0.5%, adding both compounds at each investigated concentration was beneficial for the digestion in the batch process. Therefore, the selected alcohol and aldehyde sources did not cause the expected detrimental effect on the methanogens even at the maximum amounts added in this study. Nevertheless, since the effect of the chemical compounds on methane generation has been generally concentration-dependent, the toxic effects of 1-octanol and hexanal would be better observed at higher concentrations (>0.5%), especially when their threshold levels are exceeded in anaerobic reactors digesting paper wastes.