With rapidly increased interests in biomass, diverse chemical and biological processes have been applied for biomass utilization. Fourier transform infrared (FTIR) analysis has been used for characterizing different types of biomass and their products, including natural and processed biomass. During biomass treatments, some solvents and/or catalysts can be retained and contaminate biomass. In addition, contaminants can be generated by the decomposition of biomass components. Herein, we report FTIR analyses of a series of contaminants, such as various solvents, chemicals, enzymes, and possibly formed degradation by-products in the biomass conversion process along with poplar biomass. This information helps to prevent misunderstanding the FTIR analysis results of the processed biomass.