This work demonstrates that the electrochemistry of different molecules of pharmaceutical interest, including omeprazole, ciprofloxacin, dopamine, catechol, hydroquinone, and the antioxidants tert-butylhydroquine, gallic acid, propyl gallate, and pyrogallol, is affected by the functionalization of multi-walled carbon nanotubes (MWCNTs). Voltammetric and amperometric measurements confirmed the improved analytical characteristics of the GCE modified with non-functionalized (NF) MWCNTs (as-received) in comparison with functionalized MWCNTs (F-MWCNTs). Increase in voltammetric responses (up to 10-fold), higher slope values for the amperometric detection of the analytes (up to 7-fold) and, for some molecules, widening of the linear working range, were verified. Electrochemical impedance spectroscopy measurements also revealed higher electrochemical activity of non-functionalized MWCNTs. The presence of metallic impurities on NF-MWCNTs, removed by functionalization with HNO3/H2SO4, may contribute the improved performance of NF-MWCNT-modified electrodes; however, decrease in electroactive area of F-MWCNTs has to be considered. Although acid functionalization introduced oxygenated groups on the MWCNT structure, the presence of metallic impurities (Fe and Co) and higher electroactive area of NF-MWCNTs play major role on the increase in sensitivity of the electrochemical sensors. As a conclusion, we propose the use of pristine MWCNTs to produce more sensitive amperometric sensors.