In this work a new protocol based on FTIR-microspectrometry and solvent evaporation for neurotransmitter detection is presented. In addition, a new automated sample handle support is developed and coupled to the microscope-FTIR in order to perform Dopamine and Ascorbic Acid sensing in aqueous solutions. Results show that these molecules can be detected in homogeneous and mixture samples with different ratios of concentrations (Dopamine/Ascorbic Acid) varying from 4 to 0.25. Achieved limits of detection was 3 μM and 5 μM for Dopamine and Ascorbic Acid, respectively, with this system configuration.