The surface properties of carbon based electrodes are critically important for the detection of biomolecules and can modulate electrostatic interactions, adsorption and electrocatalysis. Carbon nanotube (CNT) modified electrodes have previously been shown to have increased oxidative sensitivity and reduced overpotential for catecholamine neurotransmitters, but the effect of surface functionalities on these properties has not been characterized. In this study, we modified carbon-fiber microelectrodes (CFMEs) with three differently functionalized single-wall carbon nanotubes and measured their response to serotonin, dopamine, and ascorbic acid using fast-scan cyclic voltammetry. Both carboxylic acid functionalized and amide functionalized CNTs increased the oxidative current of CFMEs by approximately 2–6 fold for the cationic neurotransmitters serotonin and dopamine, but octadecylamine functionalized CNTs resulted in no significant signal change. Similarly, electron transfer was faster for both amide and carboxylic acid functionalized CNT modified electrodes but slower for octadecylamine CNT modified electrodes. Oxidation of ascorbic acid was only increased with carboxylic acid functionalized CNTs although all CNT-modified electrodes showed a trend towards increased reversibility for ascorbic acid. Carboxylic acid-CNT modified disk electrodes were then tested for detection of serotonin in the ventral nerve cord of a Drosophila melanogaster larva, and the increase in sensitivity was maintained in biological tissue. The functional groups of CNTs therefore modulate the electrochemical properties, and the increase in sensitivity from CNT modification facilitates measurements in biological samples.