We report a cost-efficient Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR-FTIR) method for monitoring concentrations of solutes in solutions flowing through microfluidic channels. The method allows rapid acquisition of spectra and enables chemical characterisation and concentration measurements that are independent of the flow rate of liquids. The method enables independent measurement of concentrations of solutes with distinct spectral features in mixed solutions. For the polymer solutes studied in the present work, the method has a sensitivity of at least 10 µM (0.01 wt%). We also propose the applicability of the method for the differentiation between dissolved and adsorbed amphiphilic species.